https://github.com/IGC-Advanced-Imaging-Resource/Quidwai2020_WDR35paper
Tip revision: 96b375ac31f1451dea93943fac7f563ad348ee69 authored by lauracmurphy on 20 December 2021, 15:00:56 UTC
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RadialIntensityFromCentrosomes.ijm
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<p class="ml-1 mb-2 mt-2 color-fg-default" data-show-on-error>
<svg aria-hidden="true" height="16" viewBox="0 0 16 16" version="1.1" width="16" data-view-component="true" class="octicon octicon-alert">
<path fill-rule="evenodd" d="M8.22 1.754a.25.25 0 00-.44 0L1.698 13.132a.25.25 0 00.22.368h12.164a.25.25 0 00.22-.368L8.22 1.754zm-1.763-.707c.659-1.234 2.427-1.234 3.086 0l6.082 11.378A1.75 1.75 0 0114.082 15H1.918a1.75 1.75 0 01-1.543-2.575L6.457 1.047zM9 11a1 1 0 11-2 0 1 1 0 012 0zm-.25-5.25a.75.75 0 00-1.5 0v2.5a.75.75 0 001.5 0v-2.5z"></path>
</svg>
Sorry, something went wrong.
</p>
</include-fragment>
</details-menu>
</details>
</div>
</header>
</div>
<div id="start-of-content" class="show-on-focus"></div>
<div data-pjax-replace id="js-flash-container">
<template class="js-flash-template">
<div class="flash flash-full {{ className }}">
<div class=" px-2" >
<button class="flash-close js-flash-close" type="button" aria-label="Dismiss this message">
<svg aria-hidden="true" height="16" viewBox="0 0 16 16" version="1.1" width="16" data-view-component="true" class="octicon octicon-x">
<path fill-rule="evenodd" d="M3.72 3.72a.75.75 0 011.06 0L8 6.94l3.22-3.22a.75.75 0 111.06 1.06L9.06 8l3.22 3.22a.75.75 0 11-1.06 1.06L8 9.06l-3.22 3.22a.75.75 0 01-1.06-1.06L6.94 8 3.72 4.78a.75.75 0 010-1.06z"></path>
</svg>
</button>
<div>{{ message }}</div>
</div>
</div>
</template>
</div>
<include-fragment class="js-notification-shelf-include-fragment" data-base-src="https://github.com/notifications/beta/shelf"></include-fragment>
<details class="details-reset details-overlay details-overlay-dark js-command-palette-dialog">
<summary class="command-palette-details-summary" aria-label="command palette trigger">
</summary>
<details-dialog class="command-palette-details-dialog d-flex flex-column flex-justify-center height-fit" aria-label="command palette">
<command-palette
class="command-palette color-bg-default rounded-3"
data-return-to=/IGC-Advanced-Imaging-Resource/Quidwai2020_WDR35paper/blob/main/RadialIntensityFromCentrosomes.ijm
data-user-id="36237950"
>
<input type="hidden" value="9hBmxXNz7Bl5Ai4OTlsgZ1EiSD3QxQoBToEiCX1EYqbutY6gArydWiO+n/mj5dQUuL6QrC6sRVc57kWjvGJ4rw==" data-csrf="true" class="js-graphql-csrf" />
<iframe class="d-none js-command-palette-commands" sandbox="allow-scripts allow-same-origin" srcdoc="<script crossorigin="anonymous" defer="defer" integrity="sha512-2Jz3lq/Gk0f8RePMFf+bUCfw6LwZ3nXfh3AQmMFOUj5cIW/rCeZcWRFO/q0l00bbLMcdXkpDj6KvP9Ny2qh8QA==" type="application/javascript" src="https://github.githubassets.com/assets/command-runner-d89cf796.js"></script>
" aria-hidden="true" data-url="https://github.com"></iframe>
<input type="hidden" name="color-mode-path" id="color-mode-path" value="/settings/appearance/color_mode" class="js-color-mode-path" autocomplete="off" />
<input type="hidden" value="lRlVaXFd49xkkStVXJlipscbcs7YHEQfMyxelwnnQrB3ncTz5hnzLSSNOXRG0OXSdosPxfOumU7GDvCu+98uKQ==" data-csrf="true" class="js-color-mode-csrf" />
<command-palette-mode
data-char="#"
data-scope-types="[""]"
data-placeholder="Search issues and pull requests"
></command-palette-mode>
<command-palette-mode
data-char="#"
data-scope-types="["owner","repository"]"
data-placeholder="Search issues, pull requests, discussions, and projects"
></command-palette-mode>
<command-palette-mode
data-char="!"
data-scope-types="["owner","repository"]"
data-placeholder="Search projects"
></command-palette-mode>
<command-palette-mode
data-char="@"
data-scope-types="[""]"
data-placeholder="Search or jump to a user, organization, or repository"
></command-palette-mode>
<command-palette-mode
data-char="@"
data-scope-types="["owner"]"
data-placeholder="Search or jump to a repository"
></command-palette-mode>
<command-palette-mode
data-char="/"
data-scope-types="["repository"]"
data-placeholder="Search files"
></command-palette-mode>
<command-palette-mode
data-char="?"
></command-palette-mode>
<command-palette-mode
data-char=">"
data-placeholder="Run a command"
></command-palette-mode>
<command-palette-mode
data-char=""
data-scope-types="["owner"]"
data-placeholder="Search or jump to..."
></command-palette-mode>
<command-palette-mode
class="js-command-palette-default-mode"
data-char=""
data-placeholder="Search or jump to..."
></command-palette-mode>
<command-palette-input placeholder="Search or jump to..."
>
<div class="js-search-icon d-flex flex-items-center mr-2" style="height: 26px">
<svg aria-hidden="true" height="16" viewBox="0 0 16 16" version="1.1" width="16" data-view-component="true" class="octicon octicon-search color-fg-muted">
<path fill-rule="evenodd" d="M11.5 7a4.499 4.499 0 11-8.998 0A4.499 4.499 0 0111.5 7zm-.82 4.74a6 6 0 111.06-1.06l3.04 3.04a.75.75 0 11-1.06 1.06l-3.04-3.04z"></path>
</svg>
</div>
<div class="js-spinner d-flex flex-items-center mr-2 color-fg-muted" hidden>
<svg aria-label="Loading" class="anim-rotate" viewBox="0 0 16 16" fill="none" width="16" height="16">
<circle
cx="8"
cy="8"
r="7"
stroke="currentColor"
stroke-opacity="0.25"
stroke-width="2"
vector-effect="non-scaling-stroke"
></circle>
<path
d="M15 8a7.002 7.002 0 00-7-7"
stroke="currentColor"
stroke-width="2"
stroke-linecap="round"
vector-effect="non-scaling-stroke"
></path>
</svg>
</div>
<command-palette-scope >
<command-palette-token
data-text="IGC-Advanced-Imaging-Resource"
data-id="MDEyOk9yZ2FuaXphdGlvbjM2MjM4OTYy"
data-type="owner"
data-value="IGC-Advanced-Imaging-Resource"
data-targets="command-palette-scope.tokens"
class="color-fg-default text-semibold"
>IGC-Advanced-Imaging-Res...<span class="color-fg-subtle text-normal"> / </span></command-palette-token>
<command-palette-token
data-text="Quidwai2020_WDR35paper"
data-id="MDEwOlJlcG9zaXRvcnkzMTM2NTU1MjU="
data-type="repository"
data-value="Quidwai2020_WDR35paper"
data-targets="command-palette-scope.tokens"
class="color-fg-default text-semibold"
>Quidwai2020_WDR35paper<span class="color-fg-subtle text-normal"> / </span></command-palette-token>
</command-palette-scope>
</command-palette-input>
<command-palette-item-stack id="command-palette-item-stack" class="item-stack-transition-height" role="listbox" aria-label="Command palette results">
<command-palette-tip class="color-fg-muted f6 px-3 py-1 my-2" data-type="" data-mode="" data-value="">
Type <code class="p-1 color-bg-subtle rounded-1">#</code> for issues and pull requests, <code class="p-1 color-bg-subtle rounded-1">></code> for commands, and <code class="p-1 color-bg-subtle rounded-1">?</code> for help
</command-palette-tip>
<command-palette-tip class="color-fg-muted f6 px-3 py-1 my-2" data-type="owner" data-mode="" data-value="">
Type <code class="p-1 color-bg-subtle rounded-1">#</code> for issues, pull requests, and projects, <code class="p-1 color-bg-subtle rounded-1">></code> for commands, and <code class="p-1 color-bg-subtle rounded-1">?</code> for help
</command-palette-tip>
<command-palette-tip class="color-fg-muted f6 px-3 py-1 my-2" data-type="repository" data-mode="" data-value="">
Type <code class="p-1 color-bg-subtle rounded-1">#</code> for issues, pull requests, and projects, <code class="p-1 color-bg-subtle rounded-1">/</code> for files, and <code class="p-1 color-bg-subtle rounded-1">></code> for commands
</command-palette-tip>
<command-palette-tip class="mx-3 my-2 flash flash-error d-flex flex-items-center" data-on-error>
<div>
<svg aria-hidden="true" height="16" viewBox="0 0 16 16" version="1.1" width="16" data-view-component="true" class="octicon octicon-alert">
<path fill-rule="evenodd" d="M8.22 1.754a.25.25 0 00-.44 0L1.698 13.132a.25.25 0 00.22.368h12.164a.25.25 0 00.22-.368L8.22 1.754zm-1.763-.707c.659-1.234 2.427-1.234 3.086 0l6.082 11.378A1.75 1.75 0 0114.082 15H1.918a1.75 1.75 0 01-1.543-2.575L6.457 1.047zM9 11a1 1 0 11-2 0 1 1 0 012 0zm-.25-5.25a.75.75 0 00-1.5 0v2.5a.75.75 0 001.5 0v-2.5z"></path>
</svg>
</div>
<div class="px-2">
We’ve encountered an error and some results aren't available at this time. Type a new search or try again later.
</div>
</command-palette-tip>
<command-palette-tip class="h4 color-fg-default pl-3 pb-2 pt-3" data-on-empty data-match-mode="[^?]|^$">
No results matched your search
</command-palette-tip>
<command-palette-item-group
data-group-id="top"
data-group-title="Top result"
data-group-hint=""
data-group-limits="{}"
data-targets="command-palette-item-stack.groups"
>
</command-palette-item-group>
<command-palette-item-group
data-group-id="commands"
data-group-title="Commands"
data-group-hint="Type > to filter"
data-group-limits="{}"
data-targets="command-palette-item-stack.groups"
>
</command-palette-item-group>
<command-palette-item-group
data-group-id="files"
data-group-title="Files"
data-group-hint=""
data-group-limits="{}"
data-targets="command-palette-item-stack.groups"
>
</command-palette-item-group>
<command-palette-item-group
data-group-id="pages"
data-group-title="Pages"
data-group-hint=""
data-group-limits="{"repository":10}"
data-targets="command-palette-item-stack.groups"
>
</command-palette-item-group>
<command-palette-item-group
data-group-id="access_policies"
data-group-title="Access Policies"
data-group-hint=""
data-group-limits="{}"
data-targets="command-palette-item-stack.groups"
>
</command-palette-item-group>
<command-palette-item-group
data-group-id="organizations"
data-group-title="Organizations"
data-group-hint=""
data-group-limits="{}"
data-targets="command-palette-item-stack.groups"
>
</command-palette-item-group>
<command-palette-item-group
data-group-id="repositories"
data-group-title="Repositories"
data-group-hint=""
data-group-limits="{}"
data-targets="command-palette-item-stack.groups"
>
</command-palette-item-group>
<command-palette-item-group
data-group-id="references"
data-group-title="Issues, pull requests, and discussions"
data-group-hint="Type # to filter"
data-group-limits="{}"
data-targets="command-palette-item-stack.groups"
>
</command-palette-item-group>
<command-palette-item-group
data-group-id="teams"
data-group-title="Teams"
data-group-hint=""
data-group-limits="{}"
data-targets="command-palette-item-stack.groups"
>
</command-palette-item-group>
<command-palette-item-group
data-group-id="users"
data-group-title="Users"
data-group-hint=""
data-group-limits="{}"
data-targets="command-palette-item-stack.groups"
>
</command-palette-item-group>
<command-palette-item-group
data-group-id="projects"
data-group-title="Projects"
data-group-hint=""
data-group-limits="{}"
data-targets="command-palette-item-stack.groups"
>
</command-palette-item-group>
<command-palette-item-group
data-group-id="footer"
data-group-title="Footer"
data-group-hint=""
data-group-limits="{}"
data-targets="command-palette-item-stack.groups"
>
</command-palette-item-group>
<command-palette-item-group
data-group-id="modes_help"
data-group-title="Modes"
data-group-hint=""
data-group-limits="{}"
data-targets="command-palette-item-stack.groups"
>
</command-palette-item-group>
<command-palette-item-group
data-group-id="filters_help"
data-group-title="Use filters in issues, pull requests, discussions, and projects"
data-group-hint=""
data-group-limits="{}"
data-targets="command-palette-item-stack.groups"
>
</command-palette-item-group>
</command-palette-item-stack>
<div class="js-command-local-provider-octicons" hidden>
<div data-local-provider-octicon-id="arrow-right-color-fg-muted">
<svg height="16" class="octicon octicon-arrow-right color-fg-muted" viewBox="0 0 16 16" version="1.1" width="16" aria-hidden="true"><path fill-rule="evenodd" d="M8.22 2.97a.75.75 0 011.06 0l4.25 4.25a.75.75 0 010 1.06l-4.25 4.25a.75.75 0 01-1.06-1.06l2.97-2.97H3.75a.75.75 0 010-1.5h7.44L8.22 4.03a.75.75 0 010-1.06z"></path></svg>
</div>
<div data-local-provider-octicon-id="arrow-right-color-fg-default">
<svg height="16" class="octicon octicon-arrow-right color-fg-default" viewBox="0 0 16 16" version="1.1" width="16" aria-hidden="true"><path fill-rule="evenodd" d="M8.22 2.97a.75.75 0 011.06 0l4.25 4.25a.75.75 0 010 1.06l-4.25 4.25a.75.75 0 01-1.06-1.06l2.97-2.97H3.75a.75.75 0 010-1.5h7.44L8.22 4.03a.75.75 0 010-1.06z"></path></svg>
</div>
<div data-local-provider-octicon-id="codespaces-color-fg-muted">
<svg height="16" class="octicon octicon-codespaces color-fg-muted" viewBox="0 0 16 16" version="1.1" width="16" aria-hidden="true"><path fill-rule="evenodd" d="M2 1.75C2 .784 2.784 0 3.75 0h8.5C13.216 0 14 .784 14 1.75v5a1.75 1.75 0 01-1.75 1.75h-8.5A1.75 1.75 0 012 6.75v-5zm1.75-.25a.25.25 0 00-.25.25v5c0 .138.112.25.25.25h8.5a.25.25 0 00.25-.25v-5a.25.25 0 00-.25-.25h-8.5zM0 11.25c0-.966.784-1.75 1.75-1.75h12.5c.966 0 1.75.784 1.75 1.75v3A1.75 1.75 0 0114.25 16H1.75A1.75 1.75 0 010 14.25v-3zM1.75 11a.25.25 0 00-.25.25v3c0 .138.112.25.25.25h12.5a.25.25 0 00.25-.25v-3a.25.25 0 00-.25-.25H1.75z"></path><path fill-rule="evenodd" d="M3 12.75a.75.75 0 01.75-.75h.5a.75.75 0 010 1.5h-.5a.75.75 0 01-.75-.75zm4 0a.75.75 0 01.75-.75h4.5a.75.75 0 010 1.5h-4.5a.75.75 0 01-.75-.75z"></path></svg>
</div>
<div data-local-provider-octicon-id="copy-color-fg-muted">
<svg height="16" class="octicon octicon-copy color-fg-muted" viewBox="0 0 16 16" version="1.1" width="16" aria-hidden="true"><path fill-rule="evenodd" d="M0 6.75C0 5.784.784 5 1.75 5h1.5a.75.75 0 010 1.5h-1.5a.25.25 0 00-.25.25v7.5c0 .138.112.25.25.25h7.5a.25.25 0 00.25-.25v-1.5a.75.75 0 011.5 0v1.5A1.75 1.75 0 019.25 16h-7.5A1.75 1.75 0 010 14.25v-7.5z"></path><path fill-rule="evenodd" d="M5 1.75C5 .784 5.784 0 6.75 0h7.5C15.216 0 16 .784 16 1.75v7.5A1.75 1.75 0 0114.25 11h-7.5A1.75 1.75 0 015 9.25v-7.5zm1.75-.25a.25.25 0 00-.25.25v7.5c0 .138.112.25.25.25h7.5a.25.25 0 00.25-.25v-7.5a.25.25 0 00-.25-.25h-7.5z"></path></svg>
</div>
<div data-local-provider-octicon-id="dash-color-fg-muted">
<svg height="16" class="octicon octicon-dash color-fg-muted" viewBox="0 0 16 16" version="1.1" width="16" aria-hidden="true"><path fill-rule="evenodd" d="M2 7.75A.75.75 0 012.75 7h10a.75.75 0 010 1.5h-10A.75.75 0 012 7.75z"></path></svg>
</div>
<div data-local-provider-octicon-id="file-color-fg-muted">
<svg height="16" class="octicon octicon-file color-fg-muted" viewBox="0 0 16 16" version="1.1" width="16" aria-hidden="true"><path fill-rule="evenodd" d="M3.75 1.5a.25.25 0 00-.25.25v11.5c0 .138.112.25.25.25h8.5a.25.25 0 00.25-.25V6H9.75A1.75 1.75 0 018 4.25V1.5H3.75zm5.75.56v2.19c0 .138.112.25.25.25h2.19L9.5 2.06zM2 1.75C2 .784 2.784 0 3.75 0h5.086c.464 0 .909.184 1.237.513l3.414 3.414c.329.328.513.773.513 1.237v8.086A1.75 1.75 0 0112.25 15h-8.5A1.75 1.75 0 012 13.25V1.75z"></path></svg>
</div>
<div data-local-provider-octicon-id="lock-color-fg-muted">
<svg height="16" class="octicon octicon-lock color-fg-muted" viewBox="0 0 16 16" version="1.1" width="16" aria-hidden="true"><path fill-rule="evenodd" d="M4 4v2h-.25A1.75 1.75 0 002 7.75v5.5c0 .966.784 1.75 1.75 1.75h8.5A1.75 1.75 0 0014 13.25v-5.5A1.75 1.75 0 0012.25 6H12V4a4 4 0 10-8 0zm6.5 2V4a2.5 2.5 0 00-5 0v2h5zM12 7.5h.25a.25.25 0 01.25.25v5.5a.25.25 0 01-.25.25h-8.5a.25.25 0 01-.25-.25v-5.5a.25.25 0 01.25-.25H12z"></path></svg>
</div>
<div data-local-provider-octicon-id="moon-color-fg-muted">
<svg height="16" class="octicon octicon-moon color-fg-muted" viewBox="0 0 16 16" version="1.1" width="16" aria-hidden="true"><path fill-rule="evenodd" d="M9.598 1.591a.75.75 0 01.785-.175 7 7 0 11-8.967 8.967.75.75 0 01.961-.96 5.5 5.5 0 007.046-7.046.75.75 0 01.175-.786zm1.616 1.945a7 7 0 01-7.678 7.678 5.5 5.5 0 107.678-7.678z"></path></svg>
</div>
<div data-local-provider-octicon-id="person-color-fg-muted">
<svg height="16" class="octicon octicon-person color-fg-muted" viewBox="0 0 16 16" version="1.1" width="16" aria-hidden="true"><path fill-rule="evenodd" d="M10.5 5a2.5 2.5 0 11-5 0 2.5 2.5 0 015 0zm.061 3.073a4 4 0 10-5.123 0 6.004 6.004 0 00-3.431 5.142.75.75 0 001.498.07 4.5 4.5 0 018.99 0 .75.75 0 101.498-.07 6.005 6.005 0 00-3.432-5.142z"></path></svg>
</div>
<div data-local-provider-octicon-id="pencil-color-fg-muted">
<svg height="16" class="octicon octicon-pencil color-fg-muted" viewBox="0 0 16 16" version="1.1" width="16" aria-hidden="true"><path fill-rule="evenodd" d="M11.013 1.427a1.75 1.75 0 012.474 0l1.086 1.086a1.75 1.75 0 010 2.474l-8.61 8.61c-.21.21-.47.364-.756.445l-3.251.93a.75.75 0 01-.927-.928l.929-3.25a1.75 1.75 0 01.445-.758l8.61-8.61zm1.414 1.06a.25.25 0 00-.354 0L10.811 3.75l1.439 1.44 1.263-1.263a.25.25 0 000-.354l-1.086-1.086zM11.189 6.25L9.75 4.81l-6.286 6.287a.25.25 0 00-.064.108l-.558 1.953 1.953-.558a.249.249 0 00.108-.064l6.286-6.286z"></path></svg>
</div>
<div data-local-provider-octicon-id="issue-opened-open">
<svg height="16" class="octicon octicon-issue-opened open" viewBox="0 0 16 16" version="1.1" width="16" aria-hidden="true"><path d="M8 9.5a1.5 1.5 0 100-3 1.5 1.5 0 000 3z"></path><path fill-rule="evenodd" d="M8 0a8 8 0 100 16A8 8 0 008 0zM1.5 8a6.5 6.5 0 1113 0 6.5 6.5 0 01-13 0z"></path></svg>
</div>
<div data-local-provider-octicon-id="git-pull-request-draft-color-fg-muted">
<svg height="16" class="octicon octicon-git-pull-request-draft color-fg-muted" viewBox="0 0 16 16" version="1.1" width="16" aria-hidden="true"><path fill-rule="evenodd" d="M2.5 3.25a.75.75 0 111.5 0 .75.75 0 01-1.5 0zM3.25 1a2.25 2.25 0 00-.75 4.372v5.256a2.251 2.251 0 101.5 0V5.372A2.25 2.25 0 003.25 1zm0 11a.75.75 0 100 1.5.75.75 0 000-1.5zm9.5 3a2.25 2.25 0 100-4.5 2.25 2.25 0 000 4.5zm0-3a.75.75 0 100 1.5.75.75 0 000-1.5z"></path><path d="M14 7.5a1.25 1.25 0 11-2.5 0 1.25 1.25 0 012.5 0zm0-4.25a1.25 1.25 0 11-2.5 0 1.25 1.25 0 012.5 0z"></path></svg>
</div>
<div data-local-provider-octicon-id="search-color-fg-muted">
<svg height="16" class="octicon octicon-search color-fg-muted" viewBox="0 0 16 16" version="1.1" width="16" aria-hidden="true"><path fill-rule="evenodd" d="M11.5 7a4.499 4.499 0 11-8.998 0A4.499 4.499 0 0111.5 7zm-.82 4.74a6 6 0 111.06-1.06l3.04 3.04a.75.75 0 11-1.06 1.06l-3.04-3.04z"></path></svg>
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<path fill-rule="evenodd" d="M1.679 7.932c.412-.621 1.242-1.75 2.366-2.717C5.175 4.242 6.527 3.5 8 3.5c1.473 0 2.824.742 3.955 1.715 1.124.967 1.954 2.096 2.366 2.717a.119.119 0 010 .136c-.412.621-1.242 1.75-2.366 2.717C10.825 11.758 9.473 12.5 8 12.5c-1.473 0-2.824-.742-3.955-1.715C2.92 9.818 2.09 8.69 1.679 8.068a.119.119 0 010-.136zM8 2c-1.981 0-3.67.992-4.933 2.078C1.797 5.169.88 6.423.43 7.1a1.619 1.619 0 000 1.798c.45.678 1.367 1.932 2.637 3.024C4.329 13.008 6.019 14 8 14c1.981 0 3.67-.992 4.933-2.078 1.27-1.091 2.187-2.345 2.637-3.023a1.619 1.619 0 000-1.798c-.45-.678-1.367-1.932-2.637-3.023C11.671 2.992 9.981 2 8 2zm0 8a2 2 0 100-4 2 2 0 000 4z"></path>
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Unwatch
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<span
hidden
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Stop ignoring
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<span
data-target="notifications-list-subscription-form.watchButtonCopy"
>
<svg aria-hidden="true" height="16" viewBox="0 0 16 16" version="1.1" width="16" data-view-component="true" class="octicon octicon-eye">
<path fill-rule="evenodd" d="M1.679 7.932c.412-.621 1.242-1.75 2.366-2.717C5.175 4.242 6.527 3.5 8 3.5c1.473 0 2.824.742 3.955 1.715 1.124.967 1.954 2.096 2.366 2.717a.119.119 0 010 .136c-.412.621-1.242 1.75-2.366 2.717C10.825 11.758 9.473 12.5 8 12.5c-1.473 0-2.824-.742-3.955-1.715C2.92 9.818 2.09 8.69 1.679 8.068a.119.119 0 010-.136zM8 2c-1.981 0-3.67.992-4.933 2.078C1.797 5.169.88 6.423.43 7.1a1.619 1.619 0 000 1.798c.45.678 1.367 1.932 2.637 3.024C4.329 13.008 6.019 14 8 14c1.981 0 3.67-.992 4.933-2.078 1.27-1.091 2.187-2.345 2.637-3.023a1.619 1.619 0 000-1.798c-.45-.678-1.367-1.932-2.637-3.023C11.671 2.992 9.981 2 8 2zm0 8a2 2 0 100-4 2 2 0 000 4z"></path>
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Watch
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<span id="repo-notifications-counter" data-target="notifications-list-subscription-form.socialCount" data-pjax-replace="true" title="1" data-view-component="true" class="Counter">1</span>
<span class="dropdown-caret"></span>
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<details-menu
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role="menu"
data-target="notifications-list-subscription-form.menu"
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<div class="SelectMenu-modal notifications-component-menu-modal">
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<h3 class="SelectMenu-title">Notifications</h3>
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<div class="SelectMenu-list">
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<path fill-rule="evenodd" d="M13.78 4.22a.75.75 0 010 1.06l-7.25 7.25a.75.75 0 01-1.06 0L2.22 9.28a.75.75 0 011.06-1.06L6 10.94l6.72-6.72a.75.75 0 011.06 0z"></path>
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</span>
<div>
<div class="f5 text-bold">
Participating and @mentions
</div>
<div class="text-small color-fg-muted text-normal pb-1">
Only receive notifications from this repository when participating or @mentioned.
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</button>
<button
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name="do"
value="subscribed"
class="SelectMenu-item flex-items-start"
role="menuitemradio"
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<span class="f5">
<svg aria-hidden="true" height="16" viewBox="0 0 16 16" version="1.1" width="16" data-view-component="true" class="octicon octicon-check SelectMenu-icon SelectMenu-icon--check">
<path fill-rule="evenodd" d="M13.78 4.22a.75.75 0 010 1.06l-7.25 7.25a.75.75 0 01-1.06 0L2.22 9.28a.75.75 0 011.06-1.06L6 10.94l6.72-6.72a.75.75 0 011.06 0z"></path>
</svg>
</span>
<div>
<div class="f5 text-bold">
All Activity
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<div class="text-small color-fg-muted text-normal pb-1">
Notified of all notifications on this repository.
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</div>
</button>
<button
type="submit"
name="do"
value="ignore"
class="SelectMenu-item flex-items-start"
role="menuitemradio"
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<span class="f5">
<svg aria-hidden="true" height="16" viewBox="0 0 16 16" version="1.1" width="16" data-view-component="true" class="octicon octicon-check SelectMenu-icon SelectMenu-icon--check">
<path fill-rule="evenodd" d="M13.78 4.22a.75.75 0 010 1.06l-7.25 7.25a.75.75 0 01-1.06 0L2.22 9.28a.75.75 0 011.06-1.06L6 10.94l6.72-6.72a.75.75 0 011.06 0z"></path>
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</span>
<div>
<div class="f5 text-bold">
Ignore
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<div class="text-small color-fg-muted text-normal pb-1">
Never be notified.
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</button>
</form>
<button
class="SelectMenu-item flex-items-start pr-3"
type="button"
role="menuitemradio"
data-target="notifications-list-subscription-form.customButton"
data-action="click:notifications-list-subscription-form#openCustomDialog"
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<span class="f5">
<svg aria-hidden="true" height="16" viewBox="0 0 16 16" version="1.1" width="16" data-view-component="true" class="octicon octicon-check SelectMenu-icon SelectMenu-icon--check">
<path fill-rule="evenodd" d="M13.78 4.22a.75.75 0 010 1.06l-7.25 7.25a.75.75 0 01-1.06 0L2.22 9.28a.75.75 0 011.06-1.06L6 10.94l6.72-6.72a.75.75 0 011.06 0z"></path>
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</span>
<div>
<div class="d-flex flex-items-start flex-justify-between">
<div class="f5 text-bold">Custom</div>
<div class="f5 pr-1">
<svg aria-hidden="true" height="16" viewBox="0 0 16 16" version="1.1" width="16" data-view-component="true" class="octicon octicon-arrow-right">
<path fill-rule="evenodd" d="M8.22 2.97a.75.75 0 011.06 0l4.25 4.25a.75.75 0 010 1.06l-4.25 4.25a.75.75 0 01-1.06-1.06l2.97-2.97H3.75a.75.75 0 010-1.5h7.44L8.22 4.03a.75.75 0 010-1.06z"></path>
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</div>
</div>
<div class="text-small color-fg-muted text-normal pb-1">
Select events you want to be notified of in addition to participating and @mentions.
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</div>
</button>
<div class="px-3 py-2 d-flex color-bg-subtle flex-items-center">
<span class="f5">
<svg aria-hidden="true" height="16" viewBox="0 0 16 16" version="1.1" width="16" data-view-component="true" class="octicon octicon-device-mobile SelectMenu-icon SelectMenu-icon--device-mobile">
<path fill-rule="evenodd" d="M3.75 0A1.75 1.75 0 002 1.75v12.5c0 .966.784 1.75 1.75 1.75h8.5A1.75 1.75 0 0014 14.25V1.75A1.75 1.75 0 0012.25 0h-8.5zM3.5 1.75a.25.25 0 01.25-.25h8.5a.25.25 0 01.25.25v12.5a.25.25 0 01-.25.25h-8.5a.25.25 0 01-.25-.25V1.75zM8 13a1 1 0 100-2 1 1 0 000 2z"></path>
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</span>
<span className="text-small color-fg-muted text-normal pb-1">
Get push notifications on <a target="_blank" rel="noopener noreferrer" href="https://apps.apple.com/app/apple-store/id1477376905?ct=watch-dropdown&mt=8&pt=524675">iOS</a> or <a target="_blank" rel="noopener noreferrer" href="https://play.google.com/store/apps/details?id=com.github.android&referrer=utm_campaign%3Dwatch-dropdown%26utm_medium%3Dweb%26utm_source%3Dgithub">Android</a>.
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</details-menu>
<details-dialog class="notifications-component-dialog " data-target="notifications-list-subscription-form.customDialog" hidden>
<div class="SelectMenu-modal notifications-component-dialog-modal overflow-visible">
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<button
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aria-label="Return to menu"
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data-action="click:notifications-list-subscription-form#closeCustomDialog"
>
<svg aria-hidden="true" height="16" viewBox="0 0 16 16" version="1.1" width="16" data-view-component="true" class="octicon octicon-arrow-left">
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Custom
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data-action="click:notifications-list-subscription-form#closeCustomDialog"
>
<svg style="position: relative; left: 2px; top: 1px" aria-hidden="true" height="16" viewBox="0 0 16 16" version="1.1" width="16" data-view-component="true" class="octicon octicon-arrow-left">
<path fill-rule="evenodd" d="M7.78 12.53a.75.75 0 01-1.06 0L2.47 8.28a.75.75 0 010-1.06l4.25-4.25a.75.75 0 011.06 1.06L4.81 7h7.44a.75.75 0 010 1.5H4.81l2.97 2.97a.75.75 0 010 1.06z"></path>
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<h1 class="pt-1 pr-4 pb-0 pl-0 f5 text-bold">
Custom
</h1>
</header>
<fieldset>
<legend>
<div class="text-small color-fg-muted pt-0 pr-3 pb-3 pl-6 pl-sm-5 border-bottom mb-3">
Select events you want to be notified of in addition to participating and @mentions.
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</legend>
<div class="form-checkbox mr-3 ml-6 ml-sm-5 mb-2 mt-0">
<label class="f5 text-normal">
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Issues
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<label class="f5 text-normal">
<input
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name="thread_types[]"
value="PullRequest"
data-targets="notifications-list-subscription-form.threadTypeCheckboxes"
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Pull requests
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<label class="f5 text-normal">
<input
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value="Release"
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Releases
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<input
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Discussions
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<span
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Security alerts
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<div class="notifications-component-dialog-overlay"></div>
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<li>
<div class="float-left">
<details class="details-reset details-overlay details-overlay-dark " >
<summary data-hydro-click="{"event_type":"repository.click","payload":{"target":"FORK_BUTTON","repository_id":313655525,"originating_url":"https://github.com/IGC-Advanced-Imaging-Resource/Quidwai2020_WDR35paper/blob/main/RadialIntensityFromCentrosomes.ijm","user_id":36237950}}" data-hydro-click-hmac="51a3108fee0e3d85f8945e7e8b22443e4a9d614a49090ca606373be286d81732" data-ga-click="Repository, show fork modal, action:blob#show; text:Fork" aria-label="Fork your own copy of IGC-Advanced-Imaging-Resource/Quidwai2020_WDR35paper to your account" data-view-component="true" class="btn-sm btn"> <svg aria-hidden="true" height="16" viewBox="0 0 16 16" version="1.1" width="16" data-view-component="true" class="octicon octicon-repo-forked mr-2">
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preload
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<div class="Box-header">
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<h1 class="Box-title">Fork Quidwai2020_WDR35paper</h1>
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<div class="text-center overflow-auto">
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<p class="f5 color-fg-muted">If this dialog fails to load, you can visit <a href="/IGC-Advanced-Imaging-Resource/Quidwai2020_WDR35paper/fork">the fork page</a> directly.</p>
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<button data-hydro-click="{"event_type":"repository.click","payload":{"target":"UNSTAR_BUTTON","repository_id":313655525,"originating_url":"https://github.com/IGC-Advanced-Imaging-Resource/Quidwai2020_WDR35paper/blob/main/RadialIntensityFromCentrosomes.ijm","user_id":36237950}}" data-hydro-click-hmac="88f1b609af4296f219c621b32781371200594a224b47f3aa6b2c43603a53f2de" data-ga-click="Repository, click unstar button, action:blob#show; text:Unstar" aria-label="Unstar this repository" type="submit" data-view-component="true" class="js-toggler-target rounded-left-2 border-right-0 btn-sm btn BtnGroup-item"> <svg aria-hidden="true" height="16" viewBox="0 0 16 16" version="1.1" width="16" data-view-component="true" class="octicon octicon-star-fill starred-button-icon d-inline-block mr-2">
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Starred
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Star
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<details id="details-77819d" data-view-component="true" class="details-reset details-overlay BtnGroup-parent js-user-list-menu d-inline-block position-relative">
<summary aria-label="Add this repository to a list" data-view-component="true" class="btn-sm btn BtnGroup-item px-2 float-none"> <svg aria-hidden="true" height="16" viewBox="0 0 16 16" version="1.1" width="16" data-view-component="true" class="octicon octicon-triangle-down ml-2 mr-n1">
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<template class="js-user-list-create-dialog-template" data-label="Create list">
<div class="Box-header">
<h2 class="Box-title">Create list</h2>
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<form class="Box-body d-flex flex-column p-3 js-user-list-form" action="/stars/lauracmurphy/lists" accept-charset="UTF-8" method="post"><input type="hidden" name="authenticity_token" value="CAaT3tinhpNTshRO8ZhJ3525jcF9wh4sJIE6HFgrzBblXkNoMw3Hr/xMJHFs1WToW+cr0v6v05Bs5OL0EGEYog==" autocomplete="off" />
<p class="color-fg-subtle mb-3">Create a list to organize your starred repositories.</p>
<input type="hidden" name="repository_id" value="{{ repositoryId }}">
<div class="form-group mx-0 mt-0 mb-2 js-user-list-input-container js-characters-remaining-container position-relative">
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<text-expander keys=":" data-emoji-url="/autocomplete/emoji">
<input
type="text"
name="user_list[name]"
class="form-control js-user-list-input js-characters-remaining-field"
placeholder="⭐️ Name this list"
value=""
aria-label="List name"
maxlength="32"
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autofocus
required
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hidden
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Name .
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<p class="mt-1 text-small float-right js-characters-remaining" data-suffix="remaining" hidden>
32 remaining
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<div class="form-group mx-0 mt-0 mb-2 js-user-list-input-container js-characters-remaining-container position-relative">
<text-expander keys=":" data-emoji-url="/autocomplete/emoji">
<textarea
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hidden
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Description .
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<p class="mt-1 text-small float-right js-characters-remaining" data-suffix="remaining" hidden>
160 remaining
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<div hidden="hidden" data-generic-message="Unable to save your list at this time." data-view-component="true" class="js-user-list-base flash flash-error mx-0 mt-0 mb-2">
.
</div> <button disabled="disabled" data-disable-invalid="true" data-submitting-message="Creating..." type="submit" data-view-component="true" class="btn-primary btn btn-block mt-2"> Create
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<p class="note mt-2 mb-0">
<strong>Tip:</strong> type <code>:</code> to add emoji to the name or description.
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<div data-view-component="true" class="Box-footer Box-row--gray text-small color-fg-muted d-flex flex-items-baseline py-2">
<span title="Feature Release Label: Beta" aria-label="Feature Release Label: Beta" data-view-component="true" class="Label Label--success Label--inline px-2 mr-2">Beta</span>
<span class="mr-1">Lists are currently in beta.</span>
<a href="/github/feedback/discussions/categories/lists-feedback">Share feedback and report bugs.</a>
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<details-menu
class="SelectMenu right-0"
src="/IGC-Advanced-Imaging-Resource/Quidwai2020_WDR35paper/lists"
role="menu"
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<button class="SelectMenu-closeButton position-absolute right-0 m-2" type="button" aria-label="Close menu" data-toggle-for="details-77819d">
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<path fill-rule="evenodd" d="M3.72 3.72a.75.75 0 011.06 0L8 6.94l3.22-3.22a.75.75 0 111.06 1.06L9.06 8l3.22 3.22a.75.75 0 11-1.06 1.06L8 9.06l-3.22 3.22a.75.75 0 01-1.06-1.06L6.94 8 3.72 4.78a.75.75 0 010-1.06z"></path>
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<div
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class="d-flex flex-column flex-1 overflow-hidden"
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<circle cx="8" cy="8" r="7" stroke="currentColor" stroke-opacity="0.25" stroke-width="2" vector-effect="non-scaling-stroke" />
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</details-menu>
</details>
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</li>
<li>
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<div id="responsive-meta-container" data-pjax-replace>
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<nav data-pjax="#js-repo-pjax-container" aria-label="Repository" data-view-component="true" class="js-repo-nav js-sidenav-container-pjax js-responsive-underlinenav overflow-hidden UnderlineNav px-3 px-md-4 px-lg-5">
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<span data-content="Projects">Projects</span>
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</a></li>
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<a id="wiki-tab" href="/IGC-Advanced-Imaging-Resource/Quidwai2020_WDR35paper/wiki" data-tab-item="i5wiki-tab" data-selected-links="repo_wiki /IGC-Advanced-Imaging-Resource/Quidwai2020_WDR35paper/wiki" data-pjax="#repo-content-pjax-container" data-hotkey="g w" data-ga-click="Repository, Navigation click, Wikis tab" data-view-component="true" class="UnderlineNav-item hx_underlinenav-item no-wrap js-responsive-underlinenav-item js-selected-navigation-item">
<svg aria-hidden="true" height="16" viewBox="0 0 16 16" version="1.1" width="16" data-view-component="true" class="octicon octicon-book UnderlineNav-octicon d-none d-sm-inline">
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<a id="security-tab" href="/IGC-Advanced-Imaging-Resource/Quidwai2020_WDR35paper/security" data-tab-item="i6security-tab" data-selected-links="security overview alerts policy token_scanning code_scanning /IGC-Advanced-Imaging-Resource/Quidwai2020_WDR35paper/security" data-pjax="#repo-content-pjax-container" data-hotkey="g s" data-ga-click="Repository, Navigation click, Security tab" data-view-component="true" class="UnderlineNav-item hx_underlinenav-item no-wrap js-responsive-underlinenav-item js-selected-navigation-item">
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<span data-content="Security">Security</span>
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<a id="insights-tab" href="/IGC-Advanced-Imaging-Resource/Quidwai2020_WDR35paper/pulse" data-tab-item="i7insights-tab" data-selected-links="repo_graphs repo_contributors dependency_graph dependabot_updates pulse people community /IGC-Advanced-Imaging-Resource/Quidwai2020_WDR35paper/pulse" data-pjax="#repo-content-pjax-container" data-ga-click="Repository, Navigation click, Insights tab" data-view-component="true" class="UnderlineNav-item hx_underlinenav-item no-wrap js-responsive-underlinenav-item js-selected-navigation-item">
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query-endpoint="/IGC-Advanced-Imaging-Resource/Quidwai2020_WDR35paper/refs"
can-create
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current-committish="bWFpbg=="
default-branch="bWFpbg=="
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<table class="highlight tab-size js-file-line-container js-code-nav-container js-tagsearch-file" data-tab-size="8" data-paste-markdown-skip data-tagsearch-lang="ImageJ Macro" data-tagsearch-path="RadialIntensityFromCentrosomes.ijm">
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<td id="L1" class="blob-num js-line-number js-code-nav-line-number" data-line-number="1"></td>
<td id="LC1" class="blob-code blob-code-inner js-file-line">/*</td>
</tr>
<tr>
<td id="L2" class="blob-num js-line-number js-code-nav-line-number" data-line-number="2"></td>
<td id="LC2" class="blob-code blob-code-inner js-file-line"> * Macro for segmenting centrosomes and measuring intensity spreading out from them radially</td>
</tr>
<tr>
<td id="L3" class="blob-num js-line-number js-code-nav-line-number" data-line-number="3"></td>
<td id="LC3" class="blob-code blob-code-inner js-file-line"> * Currently done with discrete bands enlarged from segmented centrosomes</td>
</tr>
<tr>
<td id="L4" class="blob-num js-line-number js-code-nav-line-number" data-line-number="4"></td>
<td id="LC4" class="blob-code blob-code-inner js-file-line"> * User can change fixed width of bands (in scaled units)</td>
</tr>
<tr>
<td id="L5" class="blob-num js-line-number js-code-nav-line-number" data-line-number="5"></td>
<td id="LC5" class="blob-code blob-code-inner js-file-line"> * Works on single image files, 3 channel Z-stacks.</td>
</tr>
<tr>
<td id="L6" class="blob-num js-line-number js-code-nav-line-number" data-line-number="6"></td>
<td id="LC6" class="blob-code blob-code-inner js-file-line"> * Written by Laura Murphy</td>
</tr>
<tr>
<td id="L7" class="blob-num js-line-number js-code-nav-line-number" data-line-number="7"></td>
<td id="LC7" class="blob-code blob-code-inner js-file-line"> * IGC Advanced Imaging Resource</td>
</tr>
<tr>
<td id="L8" class="blob-num js-line-number js-code-nav-line-number" data-line-number="8"></td>
<td id="LC8" class="blob-code blob-code-inner js-file-line"> * Updated November 2021 </td>
</tr>
<tr>
<td id="L9" class="blob-num js-line-number js-code-nav-line-number" data-line-number="9"></td>
<td id="LC9" class="blob-code blob-code-inner js-file-line"> */</td>
</tr>
<tr>
<td id="L10" class="blob-num js-line-number js-code-nav-line-number" data-line-number="10"></td>
<td id="LC10" class="blob-code blob-code-inner js-file-line">
</td>
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<td id="L11" class="blob-num js-line-number js-code-nav-line-number" data-line-number="11"></td>
<td id="LC11" class="blob-code blob-code-inner js-file-line">//--------------------------------//-----------------------------------------------------------------------------------</td>
</tr>
<tr>
<td id="L12" class="blob-num js-line-number js-code-nav-line-number" data-line-number="12"></td>
<td id="LC12" class="blob-code blob-code-inner js-file-line">//-- Part 0: Preparation steps: get directories from users and setting up arrays </td>
</tr>
<tr>
<td id="L13" class="blob-num js-line-number js-code-nav-line-number" data-line-number="13"></td>
<td id="LC13" class="blob-code blob-code-inner js-file-line">//--------------------------------//-----------------------------------------------------------------------------------</td>
</tr>
<tr>
<td id="L14" class="blob-num js-line-number js-code-nav-line-number" data-line-number="14"></td>
<td id="LC14" class="blob-code blob-code-inner js-file-line">
</td>
</tr>
<tr>
<td id="L15" class="blob-num js-line-number js-code-nav-line-number" data-line-number="15"></td>
<td id="LC15" class="blob-code blob-code-inner js-file-line">// -- Getting input and output folders from user input </td>
</tr>
<tr>
<td id="L16" class="blob-num js-line-number js-code-nav-line-number" data-line-number="16"></td>
<td id="LC16" class="blob-code blob-code-inner js-file-line">inputFolder = getDirectory("Choose the folder containing your images");</td>
</tr>
<tr>
<td id="L17" class="blob-num js-line-number js-code-nav-line-number" data-line-number="17"></td>
<td id="LC17" class="blob-code blob-code-inner js-file-line">outputFolder = getDirectory("Choose the folder where you want to save your results")</td>
</tr>
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<td id="L18" class="blob-num js-line-number js-code-nav-line-number" data-line-number="18"></td>
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</td>
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<td id="L19" class="blob-num js-line-number js-code-nav-line-number" data-line-number="19"></td>
<td id="LC19" class="blob-code blob-code-inner js-file-line">setBatchMode(true);</td>
</tr>
<tr>
<td id="L20" class="blob-num js-line-number js-code-nav-line-number" data-line-number="20"></td>
<td id="LC20" class="blob-code blob-code-inner js-file-line">
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<td id="L21" class="blob-num js-line-number js-code-nav-line-number" data-line-number="21"></td>
<td id="LC21" class="blob-code blob-code-inner js-file-line">// -- Produce list </td>
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<td id="L22" class="blob-num js-line-number js-code-nav-line-number" data-line-number="22"></td>
<td id="LC22" class="blob-code blob-code-inner js-file-line">dirList = newArray();</td>
</tr>
<tr>
<td id="L23" class="blob-num js-line-number js-code-nav-line-number" data-line-number="23"></td>
<td id="LC23" class="blob-code blob-code-inner js-file-line">dirList = getFileTree(inputFolder, dirList);</td>
</tr>
<tr>
<td id="L24" class="blob-num js-line-number js-code-nav-line-number" data-line-number="24"></td>
<td id="LC24" class="blob-code blob-code-inner js-file-line">
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</tr>
<tr>
<td id="L25" class="blob-num js-line-number js-code-nav-line-number" data-line-number="25"></td>
<td id="LC25" class="blob-code blob-code-inner js-file-line">// -- Message to users about how many images</td>
</tr>
<tr>
<td id="L26" class="blob-num js-line-number js-code-nav-line-number" data-line-number="26"></td>
<td id="LC26" class="blob-code blob-code-inner js-file-line">count = dirList.length;</td>
</tr>
<tr>
<td id="L27" class="blob-num js-line-number js-code-nav-line-number" data-line-number="27"></td>
<td id="LC27" class="blob-code blob-code-inner js-file-line">print("There are " + count + " files to be processed");</td>
</tr>
<tr>
<td id="L28" class="blob-num js-line-number js-code-nav-line-number" data-line-number="28"></td>
<td id="LC28" class="blob-code blob-code-inner js-file-line">
</td>
</tr>
<tr>
<td id="L29" class="blob-num js-line-number js-code-nav-line-number" data-line-number="29"></td>
<td id="LC29" class="blob-code blob-code-inner js-file-line">// -- Set up arrays for storing results later</td>
</tr>
<tr>
<td id="L30" class="blob-num js-line-number js-code-nav-line-number" data-line-number="30"></td>
<td id="LC30" class="blob-code blob-code-inner js-file-line">Filename = newArray;</td>
</tr>
<tr>
<td id="L31" class="blob-num js-line-number js-code-nav-line-number" data-line-number="31"></td>
<td id="LC31" class="blob-code blob-code-inner js-file-line">Signal_Mean = newArray(count);</td>
</tr>
<tr>
<td id="L32" class="blob-num js-line-number js-code-nav-line-number" data-line-number="32"></td>
<td id="LC32" class="blob-code blob-code-inner js-file-line">Centrosome_Mean = newArray(count);</td>
</tr>
<tr>
<td id="L33" class="blob-num js-line-number js-code-nav-line-number" data-line-number="33"></td>
<td id="LC33" class="blob-code blob-code-inner js-file-line">Band_One_Mean = newArray(count);</td>
</tr>
<tr>
<td id="L34" class="blob-num js-line-number js-code-nav-line-number" data-line-number="34"></td>
<td id="LC34" class="blob-code blob-code-inner js-file-line">Band_Two_Mean = newArray(count);</td>
</tr>
<tr>
<td id="L35" class="blob-num js-line-number js-code-nav-line-number" data-line-number="35"></td>
<td id="LC35" class="blob-code blob-code-inner js-file-line">Band_Three_Mean = newArray(count);</td>
</tr>
<tr>
<td id="L36" class="blob-num js-line-number js-code-nav-line-number" data-line-number="36"></td>
<td id="LC36" class="blob-code blob-code-inner js-file-line">Band_Four_Mean = newArray(count);</td>
</tr>
<tr>
<td id="L37" class="blob-num js-line-number js-code-nav-line-number" data-line-number="37"></td>
<td id="LC37" class="blob-code blob-code-inner js-file-line">Band_Five_Mean = newArray(count);</td>
</tr>
<tr>
<td id="L38" class="blob-num js-line-number js-code-nav-line-number" data-line-number="38"></td>
<td id="LC38" class="blob-code blob-code-inner js-file-line">
</td>
</tr>
<tr>
<td id="L39" class="blob-num js-line-number js-code-nav-line-number" data-line-number="39"></td>
<td id="LC39" class="blob-code blob-code-inner js-file-line">//--------------------------------//-----------------------------------------------------------------------------------</td>
</tr>
<tr>
<td id="L40" class="blob-num js-line-number js-code-nav-line-number" data-line-number="40"></td>
<td id="LC40" class="blob-code blob-code-inner js-file-line">//-- Part 1: Opening images and creating results directories</td>
</tr>
<tr>
<td id="L41" class="blob-num js-line-number js-code-nav-line-number" data-line-number="41"></td>
<td id="LC41" class="blob-code blob-code-inner js-file-line">//--------------------------------//-----------------------------------------------------------------------------------</td>
</tr>
<tr>
<td id="L42" class="blob-num js-line-number js-code-nav-line-number" data-line-number="42"></td>
<td id="LC42" class="blob-code blob-code-inner js-file-line">
</td>
</tr>
<tr>
<td id="L43" class="blob-num js-line-number js-code-nav-line-number" data-line-number="43"></td>
<td id="LC43" class="blob-code blob-code-inner js-file-line">// -- Using Bio-Formats to open images</td>
</tr>
<tr>
<td id="L44" class="blob-num js-line-number js-code-nav-line-number" data-line-number="44"></td>
<td id="LC44" class="blob-code blob-code-inner js-file-line">for (i = 0; i < dirList.length; i++){ </td>
</tr>
<tr>
<td id="L45" class="blob-num js-line-number js-code-nav-line-number" data-line-number="45"></td>
<td id="LC45" class="blob-code blob-code-inner js-file-line"> path = dirList[i];</td>
</tr>
<tr>
<td id="L46" class="blob-num js-line-number js-code-nav-line-number" data-line-number="46"></td>
<td id="LC46" class="blob-code blob-code-inner js-file-line"> run("Bio-Formats Macro Extensions");</td>
</tr>
<tr>
<td id="L47" class="blob-num js-line-number js-code-nav-line-number" data-line-number="47"></td>
<td id="LC47" class="blob-code blob-code-inner js-file-line"> run("Bio-Formats Importer", "open=&path color_mode=Composite rois_import=[ROI manager] view=Hyperstack stack_order=XYCZT series_1"); </td>
</tr>
<tr>
<td id="L48" class="blob-num js-line-number js-code-nav-line-number" data-line-number="48"></td>
<td id="LC48" class="blob-code blob-code-inner js-file-line">
</td>
</tr>
<tr>
<td id="L49" class="blob-num js-line-number js-code-nav-line-number" data-line-number="49"></td>
<td id="LC49" class="blob-code blob-code-inner js-file-line"> fileName = getTitle();</td>
</tr>
<tr>
<td id="L50" class="blob-num js-line-number js-code-nav-line-number" data-line-number="50"></td>
<td id="LC50" class="blob-code blob-code-inner js-file-line"> Filename = Array.concat(Filename, fileName);</td>
</tr>
<tr>
<td id="L51" class="blob-num js-line-number js-code-nav-line-number" data-line-number="51"></td>
<td id="LC51" class="blob-code blob-code-inner js-file-line"> imgName = File.nameWithoutExtension();</td>
</tr>
<tr>
<td id="L52" class="blob-num js-line-number js-code-nav-line-number" data-line-number="52"></td>
<td id="LC52" class="blob-code blob-code-inner js-file-line"> getDimensions(width, height, channels, slices, frames);</td>
</tr>
<tr>
<td id="L53" class="blob-num js-line-number js-code-nav-line-number" data-line-number="53"></td>
<td id="LC53" class="blob-code blob-code-inner js-file-line"> getPixelSize(unit, pixelWidth, pixelHeight);</td>
</tr>
<tr>
<td id="L54" class="blob-num js-line-number js-code-nav-line-number" data-line-number="54"></td>
<td id="LC54" class="blob-code blob-code-inner js-file-line">
</td>
</tr>
<tr>
<td id="L55" class="blob-num js-line-number js-code-nav-line-number" data-line-number="55"></td>
<td id="LC55" class="blob-code blob-code-inner js-file-line">//--------------------------------//-----------------------------------------------------------------------------------</td>
</tr>
<tr>
<td id="L56" class="blob-num js-line-number js-code-nav-line-number" data-line-number="56"></td>
<td id="LC56" class="blob-code blob-code-inner js-file-line">//-- Part 2: File processing</td>
</tr>
<tr>
<td id="L57" class="blob-num js-line-number js-code-nav-line-number" data-line-number="57"></td>
<td id="LC57" class="blob-code blob-code-inner js-file-line">//--------------------------------//-----------------------------------------------------------------------------------</td>
</tr>
<tr>
<td id="L58" class="blob-num js-line-number js-code-nav-line-number" data-line-number="58"></td>
<td id="LC58" class="blob-code blob-code-inner js-file-line">
</td>
</tr>
<tr>
<td id="L59" class="blob-num js-line-number js-code-nav-line-number" data-line-number="59"></td>
<td id="LC59" class="blob-code blob-code-inner js-file-line"> projection = "Max Intensity"; //Choose from 'Max Intensity', 'Average Intensity', 'Sum Slices '</td>
</tr>
<tr>
<td id="L60" class="blob-num js-line-number js-code-nav-line-number" data-line-number="60"></td>
<td id="LC60" class="blob-code blob-code-inner js-file-line">
</td>
</tr>
<tr>
<td id="L61" class="blob-num js-line-number js-code-nav-line-number" data-line-number="61"></td>
<td id="LC61" class="blob-code blob-code-inner js-file-line"> // Get sum slices stack, set channel LUTs</td>
</tr>
<tr>
<td id="L62" class="blob-num js-line-number js-code-nav-line-number" data-line-number="62"></td>
<td id="LC62" class="blob-code blob-code-inner js-file-line"> Stack.setChannel(1);</td>
</tr>
<tr>
<td id="L63" class="blob-num js-line-number js-code-nav-line-number" data-line-number="63"></td>
<td id="LC63" class="blob-code blob-code-inner js-file-line"> run("Blue"); </td>
</tr>
<tr>
<td id="L64" class="blob-num js-line-number js-code-nav-line-number" data-line-number="64"></td>
<td id="LC64" class="blob-code blob-code-inner js-file-line"> Stack.setChannel(3);</td>
</tr>
<tr>
<td id="L65" class="blob-num js-line-number js-code-nav-line-number" data-line-number="65"></td>
<td id="LC65" class="blob-code blob-code-inner js-file-line"> run("Red"); </td>
</tr>
<tr>
<td id="L66" class="blob-num js-line-number js-code-nav-line-number" data-line-number="66"></td>
<td id="LC66" class="blob-code blob-code-inner js-file-line"> run("Z Project...", "projection=[Max Intensity]");</td>
</tr>
<tr>
<td id="L67" class="blob-num js-line-number js-code-nav-line-number" data-line-number="67"></td>
<td id="LC67" class="blob-code blob-code-inner js-file-line"> rename("MProjection");</td>
</tr>
<tr>
<td id="L68" class="blob-num js-line-number js-code-nav-line-number" data-line-number="68"></td>
<td id="LC68" class="blob-code blob-code-inner js-file-line">
</td>
</tr>
<tr>
<td id="L69" class="blob-num js-line-number js-code-nav-line-number" data-line-number="69"></td>
<td id="LC69" class="blob-code blob-code-inner js-file-line"> selectWindow(fileName);</td>
</tr>
<tr>
<td id="L70" class="blob-num js-line-number js-code-nav-line-number" data-line-number="70"></td>
<td id="LC70" class="blob-code blob-code-inner js-file-line"> Stack.setChannel(1);</td>
</tr>
<tr>
<td id="L71" class="blob-num js-line-number js-code-nav-line-number" data-line-number="71"></td>
<td id="LC71" class="blob-code blob-code-inner js-file-line"> run("Blue"); </td>
</tr>
<tr>
<td id="L72" class="blob-num js-line-number js-code-nav-line-number" data-line-number="72"></td>
<td id="LC72" class="blob-code blob-code-inner js-file-line"> Stack.setChannel(3);</td>
</tr>
<tr>
<td id="L73" class="blob-num js-line-number js-code-nav-line-number" data-line-number="73"></td>
<td id="LC73" class="blob-code blob-code-inner js-file-line"> run("Red"); </td>
</tr>
<tr>
<td id="L74" class="blob-num js-line-number js-code-nav-line-number" data-line-number="74"></td>
<td id="LC74" class="blob-code blob-code-inner js-file-line"> run("Z Project...", "projection=[" + projection + "]");</td>
</tr>
<tr>
<td id="L75" class="blob-num js-line-number js-code-nav-line-number" data-line-number="75"></td>
<td id="LC75" class="blob-code blob-code-inner js-file-line"> run("Duplicate...", "duplicate"); </td>
</tr>
<tr>
<td id="L76" class="blob-num js-line-number js-code-nav-line-number" data-line-number="76"></td>
<td id="LC76" class="blob-code blob-code-inner js-file-line"> rename("Projection");</td>
</tr>
<tr>
<td id="L77" class="blob-num js-line-number js-code-nav-line-number" data-line-number="77"></td>
<td id="LC77" class="blob-code blob-code-inner js-file-line"> </td>
</tr>
<tr>
<td id="L78" class="blob-num js-line-number js-code-nav-line-number" data-line-number="78"></td>
<td id="LC78" class="blob-code blob-code-inner js-file-line"> selectWindow(fileName);</td>
</tr>
<tr>
<td id="L79" class="blob-num js-line-number js-code-nav-line-number" data-line-number="79"></td>
<td id="LC79" class="blob-code blob-code-inner js-file-line"> run("Close");</td>
</tr>
<tr>
<td id="L80" class="blob-num js-line-number js-code-nav-line-number" data-line-number="80"></td>
<td id="LC80" class="blob-code blob-code-inner js-file-line">
</td>
</tr>
<tr>
<td id="L81" class="blob-num js-line-number js-code-nav-line-number" data-line-number="81"></td>
<td id="LC81" class="blob-code blob-code-inner js-file-line"> // Splits channels and renames based on signal</td>
</tr>
<tr>
<td id="L82" class="blob-num js-line-number js-code-nav-line-number" data-line-number="82"></td>
<td id="LC82" class="blob-code blob-code-inner js-file-line"> selectWindow("MProjection");</td>
</tr>
<tr>
<td id="L83" class="blob-num js-line-number js-code-nav-line-number" data-line-number="83"></td>
<td id="LC83" class="blob-code blob-code-inner js-file-line"> run("Duplicate...", "duplicate"); </td>
</tr>
<tr>
<td id="L84" class="blob-num js-line-number js-code-nav-line-number" data-line-number="84"></td>
<td id="LC84" class="blob-code blob-code-inner js-file-line"> rename("Active");</td>
</tr>
<tr>
<td id="L85" class="blob-num js-line-number js-code-nav-line-number" data-line-number="85"></td>
<td id="LC85" class="blob-code blob-code-inner js-file-line"> run("Split Channels"); </td>
</tr>
<tr>
<td id="L86" class="blob-num js-line-number js-code-nav-line-number" data-line-number="86"></td>
<td id="LC86" class="blob-code blob-code-inner js-file-line"> selectWindow("C1-Active");</td>
</tr>
<tr>
<td id="L87" class="blob-num js-line-number js-code-nav-line-number" data-line-number="87"></td>
<td id="LC87" class="blob-code blob-code-inner js-file-line"> rename("Nuclei");</td>
</tr>
<tr>
<td id="L88" class="blob-num js-line-number js-code-nav-line-number" data-line-number="88"></td>
<td id="LC88" class="blob-code blob-code-inner js-file-line"> selectWindow("C2-Active");</td>
</tr>
<tr>
<td id="L89" class="blob-num js-line-number js-code-nav-line-number" data-line-number="89"></td>
<td id="LC89" class="blob-code blob-code-inner js-file-line"> run("Close");</td>
</tr>
<tr>
<td id="L90" class="blob-num js-line-number js-code-nav-line-number" data-line-number="90"></td>
<td id="LC90" class="blob-code blob-code-inner js-file-line"> selectWindow("C3-Active");</td>
</tr>
<tr>
<td id="L91" class="blob-num js-line-number js-code-nav-line-number" data-line-number="91"></td>
<td id="LC91" class="blob-code blob-code-inner js-file-line"> rename("Centrosomes");</td>
</tr>
<tr>
<td id="L92" class="blob-num js-line-number js-code-nav-line-number" data-line-number="92"></td>
<td id="LC92" class="blob-code blob-code-inner js-file-line">
</td>
</tr>
<tr>
<td id="L93" class="blob-num js-line-number js-code-nav-line-number" data-line-number="93"></td>
<td id="LC93" class="blob-code blob-code-inner js-file-line"> selectWindow("Projection");</td>
</tr>
<tr>
<td id="L94" class="blob-num js-line-number js-code-nav-line-number" data-line-number="94"></td>
<td id="LC94" class="blob-code blob-code-inner js-file-line"> run("Duplicate...", "duplicate"); </td>
</tr>
<tr>
<td id="L95" class="blob-num js-line-number js-code-nav-line-number" data-line-number="95"></td>
<td id="LC95" class="blob-code blob-code-inner js-file-line"> rename("Active");</td>
</tr>
<tr>
<td id="L96" class="blob-num js-line-number js-code-nav-line-number" data-line-number="96"></td>
<td id="LC96" class="blob-code blob-code-inner js-file-line"> run("Split Channels"); </td>
</tr>
<tr>
<td id="L97" class="blob-num js-line-number js-code-nav-line-number" data-line-number="97"></td>
<td id="LC97" class="blob-code blob-code-inner js-file-line"> selectWindow("C1-Active");</td>
</tr>
<tr>
<td id="L98" class="blob-num js-line-number js-code-nav-line-number" data-line-number="98"></td>
<td id="LC98" class="blob-code blob-code-inner js-file-line"> run("Close");</td>
</tr>
<tr>
<td id="L99" class="blob-num js-line-number js-code-nav-line-number" data-line-number="99"></td>
<td id="LC99" class="blob-code blob-code-inner js-file-line"> selectWindow("C2-Active");</td>
</tr>
<tr>
<td id="L100" class="blob-num js-line-number js-code-nav-line-number" data-line-number="100"></td>
<td id="LC100" class="blob-code blob-code-inner js-file-line"> rename("Signal");</td>
</tr>
<tr>
<td id="L101" class="blob-num js-line-number js-code-nav-line-number" data-line-number="101"></td>
<td id="LC101" class="blob-code blob-code-inner js-file-line"> selectWindow("C3-Active");</td>
</tr>
<tr>
<td id="L102" class="blob-num js-line-number js-code-nav-line-number" data-line-number="102"></td>
<td id="LC102" class="blob-code blob-code-inner js-file-line"> run("Close");</td>
</tr>
<tr>
<td id="L103" class="blob-num js-line-number js-code-nav-line-number" data-line-number="103"></td>
<td id="LC103" class="blob-code blob-code-inner js-file-line"> </td>
</tr>
<tr>
<td id="L104" class="blob-num js-line-number js-code-nav-line-number" data-line-number="104"></td>
<td id="LC104" class="blob-code blob-code-inner js-file-line">//--------------------------------//-----------------------------------------------------------------------------------</td>
</tr>
<tr>
<td id="L105" class="blob-num js-line-number js-code-nav-line-number" data-line-number="105"></td>
<td id="LC105" class="blob-code blob-code-inner js-file-line">//-- Part 3: Segmenting centrosomes</td>
</tr>
<tr>
<td id="L106" class="blob-num js-line-number js-code-nav-line-number" data-line-number="106"></td>
<td id="LC106" class="blob-code blob-code-inner js-file-line">//--------------------------------//-----------------------------------------------------------------------------------</td>
</tr>
<tr>
<td id="L107" class="blob-num js-line-number js-code-nav-line-number" data-line-number="107"></td>
<td id="LC107" class="blob-code blob-code-inner js-file-line">
</td>
</tr>
<tr>
<td id="L108" class="blob-num js-line-number js-code-nav-line-number" data-line-number="108"></td>
<td id="LC108" class="blob-code blob-code-inner js-file-line"> // -- Segmentation with centrosomes, may need changed (think about sum vs MIP projections, may want a different threshold and size limit)</td>
</tr>
<tr>
<td id="L109" class="blob-num js-line-number js-code-nav-line-number" data-line-number="109"></td>
<td id="LC109" class="blob-code blob-code-inner js-file-line"> selectWindow("Centrosomes");</td>
</tr>
<tr>
<td id="L110" class="blob-num js-line-number js-code-nav-line-number" data-line-number="110"></td>
<td id="LC110" class="blob-code blob-code-inner js-file-line"> setAutoThreshold("RenyiEntropy dark");</td>
</tr>
<tr>
<td id="L111" class="blob-num js-line-number js-code-nav-line-number" data-line-number="111"></td>
<td id="LC111" class="blob-code blob-code-inner js-file-line"> run("Convert to Mask");</td>
</tr>
<tr>
<td id="L112" class="blob-num js-line-number js-code-nav-line-number" data-line-number="112"></td>
<td id="LC112" class="blob-code blob-code-inner js-file-line"> run("Watershed");</td>
</tr>
<tr>
<td id="L113" class="blob-num js-line-number js-code-nav-line-number" data-line-number="113"></td>
<td id="LC113" class="blob-code blob-code-inner js-file-line"> makeRectangle(15,15,getWidth-30, getHeight-30);</td>
</tr>
<tr>
<td id="L114" class="blob-num js-line-number js-code-nav-line-number" data-line-number="114"></td>
<td id="LC114" class="blob-code blob-code-inner js-file-line"> run("Analyze Particles...", "size=0.1-Infinity exclude add");</td>
</tr>
<tr>
<td id="L115" class="blob-num js-line-number js-code-nav-line-number" data-line-number="115"></td>
<td id="LC115" class="blob-code blob-code-inner js-file-line"> run("Set Measurements...", "area centroid display redirect=None decimal=4");</td>
</tr>
<tr>
<td id="L116" class="blob-num js-line-number js-code-nav-line-number" data-line-number="116"></td>
<td id="LC116" class="blob-code blob-code-inner js-file-line">
</td>
</tr>
<tr>
<td id="L117" class="blob-num js-line-number js-code-nav-line-number" data-line-number="117"></td>
<td id="LC117" class="blob-code blob-code-inner js-file-line"> // -- Save image with centrosome ROIs</td>
</tr>
<tr>
<td id="L118" class="blob-num js-line-number js-code-nav-line-number" data-line-number="118"></td>
<td id="LC118" class="blob-code blob-code-inner js-file-line"> selectWindow("MProjection");</td>
</tr>
<tr>
<td id="L119" class="blob-num js-line-number js-code-nav-line-number" data-line-number="119"></td>
<td id="LC119" class="blob-code blob-code-inner js-file-line"> Stack.setChannel(1);</td>
</tr>
<tr>
<td id="L120" class="blob-num js-line-number js-code-nav-line-number" data-line-number="120"></td>
<td id="LC120" class="blob-code blob-code-inner js-file-line"> run("Enhance Contrast...", "saturated=0.3 normalize");</td>
</tr>
<tr>
<td id="L121" class="blob-num js-line-number js-code-nav-line-number" data-line-number="121"></td>
<td id="LC121" class="blob-code blob-code-inner js-file-line"> Stack.setChannel(2);</td>
</tr>
<tr>
<td id="L122" class="blob-num js-line-number js-code-nav-line-number" data-line-number="122"></td>
<td id="LC122" class="blob-code blob-code-inner js-file-line"> run("Enhance Contrast...", "saturated=0.3 normalize");</td>
</tr>
<tr>
<td id="L123" class="blob-num js-line-number js-code-nav-line-number" data-line-number="123"></td>
<td id="LC123" class="blob-code blob-code-inner js-file-line"> Stack.setChannel(3);</td>
</tr>
<tr>
<td id="L124" class="blob-num js-line-number js-code-nav-line-number" data-line-number="124"></td>
<td id="LC124" class="blob-code blob-code-inner js-file-line"> run("Enhance Contrast...", "saturated=0.3 normalize");</td>
</tr>
<tr>
<td id="L125" class="blob-num js-line-number js-code-nav-line-number" data-line-number="125"></td>
<td id="LC125" class="blob-code blob-code-inner js-file-line"> run("RGB Color");</td>
</tr>
<tr>
<td id="L126" class="blob-num js-line-number js-code-nav-line-number" data-line-number="126"></td>
<td id="LC126" class="blob-code blob-code-inner js-file-line"> roiManager("Show All without labels");</td>
</tr>
<tr>
<td id="L127" class="blob-num js-line-number js-code-nav-line-number" data-line-number="127"></td>
<td id="LC127" class="blob-code blob-code-inner js-file-line"> run("Flatten");</td>
</tr>
<tr>
<td id="L128" class="blob-num js-line-number js-code-nav-line-number" data-line-number="128"></td>
<td id="LC128" class="blob-code blob-code-inner js-file-line"> saveAs("Tiff", outputFolder + File.separator + imgName + "_Centrosomes.tif");</td>
</tr>
<tr>
<td id="L129" class="blob-num js-line-number js-code-nav-line-number" data-line-number="129"></td>
<td id="LC129" class="blob-code blob-code-inner js-file-line">
</td>
</tr>
<tr>
<td id="L130" class="blob-num js-line-number js-code-nav-line-number" data-line-number="130"></td>
<td id="LC130" class="blob-code blob-code-inner js-file-line"> // -- Print message to tell user how many centrosomes have been detected</td>
</tr>
<tr>
<td id="L131" class="blob-num js-line-number js-code-nav-line-number" data-line-number="131"></td>
<td id="LC131" class="blob-code blob-code-inner js-file-line"> centrosomes = roiManager("Count");</td>
</tr>
<tr>
<td id="L132" class="blob-num js-line-number js-code-nav-line-number" data-line-number="132"></td>
<td id="LC132" class="blob-code blob-code-inner js-file-line"> print(imgName + " has a pixel size of " + pixelWidth + " and has " + centrosomes + " centrosomes"); </td>
</tr>
<tr>
<td id="L133" class="blob-num js-line-number js-code-nav-line-number" data-line-number="133"></td>
<td id="LC133" class="blob-code blob-code-inner js-file-line">
</td>
</tr>
<tr>
<td id="L134" class="blob-num js-line-number js-code-nav-line-number" data-line-number="134"></td>
<td id="LC134" class="blob-code blob-code-inner js-file-line">//--------------------------------//-----------------------------------------------------------------------------------</td>
</tr>
<tr>
<td id="L135" class="blob-num js-line-number js-code-nav-line-number" data-line-number="135"></td>
<td id="LC135" class="blob-code blob-code-inner js-file-line">//-- Part 4: Create bands from segmentation and measure them on the signal channel</td>
</tr>
<tr>
<td id="L136" class="blob-num js-line-number js-code-nav-line-number" data-line-number="136"></td>
<td id="LC136" class="blob-code blob-code-inner js-file-line">//-- Currently bands are one pixel and five pixels around centrosome but can be changed</td>
</tr>
<tr>
<td id="L137" class="blob-num js-line-number js-code-nav-line-number" data-line-number="137"></td>
<td id="LC137" class="blob-code blob-code-inner js-file-line">//-- Do we maybe want to make it so that total intensity in that area is 100% and how much it drops over time?</td>
</tr>
<tr>
<td id="L138" class="blob-num js-line-number js-code-nav-line-number" data-line-number="138"></td>
<td id="LC138" class="blob-code blob-code-inner js-file-line">//--------------------------------//-----------------------------------------------------------------------------------</td>
</tr>
<tr>
<td id="L139" class="blob-num js-line-number js-code-nav-line-number" data-line-number="139"></td>
<td id="LC139" class="blob-code blob-code-inner js-file-line">
</td>
</tr>
<tr>
<td id="L140" class="blob-num js-line-number js-code-nav-line-number" data-line-number="140"></td>
<td id="LC140" class="blob-code blob-code-inner js-file-line"> selectWindow("Signal");</td>
</tr>
<tr>
<td id="L141" class="blob-num js-line-number js-code-nav-line-number" data-line-number="141"></td>
<td id="LC141" class="blob-code blob-code-inner js-file-line"> rename(imgName);</td>
</tr>
<tr>
<td id="L142" class="blob-num js-line-number js-code-nav-line-number" data-line-number="142"></td>
<td id="LC142" class="blob-code blob-code-inner js-file-line"> getStatistics(area, Signal_Mean[i], min, max, std, histogram);</td>
</tr>
<tr>
<td id="L143" class="blob-num js-line-number js-code-nav-line-number" data-line-number="143"></td>
<td id="LC143" class="blob-code blob-code-inner js-file-line"> </td>
</tr>
<tr>
<td id="L144" class="blob-num js-line-number js-code-nav-line-number" data-line-number="144"></td>
<td id="LC144" class="blob-code blob-code-inner js-file-line"> // -- Create arrays to store results</td>
</tr>
<tr>
<td id="L145" class="blob-num js-line-number js-code-nav-line-number" data-line-number="145"></td>
<td id="LC145" class="blob-code blob-code-inner js-file-line"> Label = newArray(centrosomes);</td>
</tr>
<tr>
<td id="L146" class="blob-num js-line-number js-code-nav-line-number" data-line-number="146"></td>
<td id="LC146" class="blob-code blob-code-inner js-file-line"> Centrosome = newArray(centrosomes);</td>
</tr>
<tr>
<td id="L147" class="blob-num js-line-number js-code-nav-line-number" data-line-number="147"></td>
<td id="LC147" class="blob-code blob-code-inner js-file-line"> Band_One = newArray(centrosomes);</td>
</tr>
<tr>
<td id="L148" class="blob-num js-line-number js-code-nav-line-number" data-line-number="148"></td>
<td id="LC148" class="blob-code blob-code-inner js-file-line"> Band_Two = newArray(centrosomes);</td>
</tr>
<tr>
<td id="L149" class="blob-num js-line-number js-code-nav-line-number" data-line-number="149"></td>
<td id="LC149" class="blob-code blob-code-inner js-file-line"> Band_Three = newArray(centrosomes);</td>
</tr>
<tr>
<td id="L150" class="blob-num js-line-number js-code-nav-line-number" data-line-number="150"></td>
<td id="LC150" class="blob-code blob-code-inner js-file-line"> Band_Four = newArray(centrosomes);</td>
</tr>
<tr>
<td id="L151" class="blob-num js-line-number js-code-nav-line-number" data-line-number="151"></td>
<td id="LC151" class="blob-code blob-code-inner js-file-line"> Band_Five = newArray(centrosomes);</td>
</tr>
<tr>
<td id="L152" class="blob-num js-line-number js-code-nav-line-number" data-line-number="152"></td>
<td id="LC152" class="blob-code blob-code-inner js-file-line">
</td>
</tr>
<tr>
<td id="L153" class="blob-num js-line-number js-code-nav-line-number" data-line-number="153"></td>
<td id="LC153" class="blob-code blob-code-inner js-file-line"> radius = 0.5; //change this number to change band size</td>
</tr>
<tr>
<td id="L154" class="blob-num js-line-number js-code-nav-line-number" data-line-number="154"></td>
<td id="LC154" class="blob-code blob-code-inner js-file-line">
</td>
</tr>
<tr>
<td id="L155" class="blob-num js-line-number js-code-nav-line-number" data-line-number="155"></td>
<td id="LC155" class="blob-code blob-code-inner js-file-line"> for(j = 0; j < centrosomes; j++){</td>
</tr>
<tr>
<td id="L156" class="blob-num js-line-number js-code-nav-line-number" data-line-number="156"></td>
<td id="LC156" class="blob-code blob-code-inner js-file-line"> roiManager("Select", j); </td>
</tr>
<tr>
<td id="L157" class="blob-num js-line-number js-code-nav-line-number" data-line-number="157"></td>
<td id="LC157" class="blob-code blob-code-inner js-file-line"> roiManager("Rename", "Centrosome_"+(j+1));</td>
</tr>
<tr>
<td id="L158" class="blob-num js-line-number js-code-nav-line-number" data-line-number="158"></td>
<td id="LC158" class="blob-code blob-code-inner js-file-line"> Label[j] = "Centrosome_"+(j+1);</td>
</tr>
<tr>
<td id="L159" class="blob-num js-line-number js-code-nav-line-number" data-line-number="159"></td>
<td id="LC159" class="blob-code blob-code-inner js-file-line"> roiManager("Set Color", "red");</td>
</tr>
<tr>
<td id="L160" class="blob-num js-line-number js-code-nav-line-number" data-line-number="160"></td>
<td id="LC160" class="blob-code blob-code-inner js-file-line"> getStatistics(area, Centrosome[j], min, max, std, histogram);</td>
</tr>
<tr>
<td id="L161" class="blob-num js-line-number js-code-nav-line-number" data-line-number="161"></td>
<td id="LC161" class="blob-code blob-code-inner js-file-line">
</td>
</tr>
<tr>
<td id="L162" class="blob-num js-line-number js-code-nav-line-number" data-line-number="162"></td>
<td id="LC162" class="blob-code blob-code-inner js-file-line"> roiManager("Select", j);</td>
</tr>
<tr>
<td id="L163" class="blob-num js-line-number js-code-nav-line-number" data-line-number="163"></td>
<td id="LC163" class="blob-code blob-code-inner js-file-line"> run("Enlarge...", "enlarge=" + radius);</td>
</tr>
<tr>
<td id="L164" class="blob-num js-line-number js-code-nav-line-number" data-line-number="164"></td>
<td id="LC164" class="blob-code blob-code-inner js-file-line"> Roi.setName("Centrosome_" + (j+1) + ": Circle_1");</td>
</tr>
<tr>
<td id="L165" class="blob-num js-line-number js-code-nav-line-number" data-line-number="165"></td>
<td id="LC165" class="blob-code blob-code-inner js-file-line"> roiManager("Add");</td>
</tr>
<tr>
<td id="L166" class="blob-num js-line-number js-code-nav-line-number" data-line-number="166"></td>
<td id="LC166" class="blob-code blob-code-inner js-file-line"> roiManager("Select", newArray(j, roiManager("Count")-1));</td>
</tr>
<tr>
<td id="L167" class="blob-num js-line-number js-code-nav-line-number" data-line-number="167"></td>
<td id="LC167" class="blob-code blob-code-inner js-file-line"> roiManager("XOR");</td>
</tr>
<tr>
<td id="L168" class="blob-num js-line-number js-code-nav-line-number" data-line-number="168"></td>
<td id="LC168" class="blob-code blob-code-inner js-file-line"> Roi.setName("Centrosome_" + (j+1) + ": Band_1");</td>
</tr>
<tr>
<td id="L169" class="blob-num js-line-number js-code-nav-line-number" data-line-number="169"></td>
<td id="LC169" class="blob-code blob-code-inner js-file-line"> roiManager("Set Color", "orange");</td>
</tr>
<tr>
<td id="L170" class="blob-num js-line-number js-code-nav-line-number" data-line-number="170"></td>
<td id="LC170" class="blob-code blob-code-inner js-file-line"> roiManager("Add");</td>
</tr>
<tr>
<td id="L171" class="blob-num js-line-number js-code-nav-line-number" data-line-number="171"></td>
<td id="LC171" class="blob-code blob-code-inner js-file-line"> roiManager("Select", roiManager("Count")-1);</td>
</tr>
<tr>
<td id="L172" class="blob-num js-line-number js-code-nav-line-number" data-line-number="172"></td>
<td id="LC172" class="blob-code blob-code-inner js-file-line"> getStatistics(area, Band_One[j], min, max, std, histogram);</td>
</tr>
<tr>
<td id="L173" class="blob-num js-line-number js-code-nav-line-number" data-line-number="173"></td>
<td id="LC173" class="blob-code blob-code-inner js-file-line">
</td>
</tr>
<tr>
<td id="L174" class="blob-num js-line-number js-code-nav-line-number" data-line-number="174"></td>
<td id="LC174" class="blob-code blob-code-inner js-file-line"> roiManager("Select", roiManager("Count")-2);</td>
</tr>
<tr>
<td id="L175" class="blob-num js-line-number js-code-nav-line-number" data-line-number="175"></td>
<td id="LC175" class="blob-code blob-code-inner js-file-line"> run("Enlarge...", "enlarge=" + radius);</td>
</tr>
<tr>
<td id="L176" class="blob-num js-line-number js-code-nav-line-number" data-line-number="176"></td>
<td id="LC176" class="blob-code blob-code-inner js-file-line"> Roi.setName("Centrosome_" + (j+1) + ": Circle_2");</td>
</tr>
<tr>
<td id="L177" class="blob-num js-line-number js-code-nav-line-number" data-line-number="177"></td>
<td id="LC177" class="blob-code blob-code-inner js-file-line"> roiManager("Add");</td>
</tr>
<tr>
<td id="L178" class="blob-num js-line-number js-code-nav-line-number" data-line-number="178"></td>
<td id="LC178" class="blob-code blob-code-inner js-file-line"> roiManager("Select", newArray(roiManager("Count")-3, roiManager("Count")-1));</td>
</tr>
<tr>
<td id="L179" class="blob-num js-line-number js-code-nav-line-number" data-line-number="179"></td>
<td id="LC179" class="blob-code blob-code-inner js-file-line"> roiManager("XOR");</td>
</tr>
<tr>
<td id="L180" class="blob-num js-line-number js-code-nav-line-number" data-line-number="180"></td>
<td id="LC180" class="blob-code blob-code-inner js-file-line"> Roi.setName("Centrosome_" + (j+1) + ": Band_2");</td>
</tr>
<tr>
<td id="L181" class="blob-num js-line-number js-code-nav-line-number" data-line-number="181"></td>
<td id="LC181" class="blob-code blob-code-inner js-file-line"> roiManager("Set Color", "orange");</td>
</tr>
<tr>
<td id="L182" class="blob-num js-line-number js-code-nav-line-number" data-line-number="182"></td>
<td id="LC182" class="blob-code blob-code-inner js-file-line"> roiManager("Add");</td>
</tr>
<tr>
<td id="L183" class="blob-num js-line-number js-code-nav-line-number" data-line-number="183"></td>
<td id="LC183" class="blob-code blob-code-inner js-file-line"> roiManager("Select", roiManager("Count")-1);</td>
</tr>
<tr>
<td id="L184" class="blob-num js-line-number js-code-nav-line-number" data-line-number="184"></td>
<td id="LC184" class="blob-code blob-code-inner js-file-line"> getStatistics(area, Band_Two[j], min, max, std, histogram);</td>
</tr>
<tr>
<td id="L185" class="blob-num js-line-number js-code-nav-line-number" data-line-number="185"></td>
<td id="LC185" class="blob-code blob-code-inner js-file-line">
</td>
</tr>
<tr>
<td id="L186" class="blob-num js-line-number js-code-nav-line-number" data-line-number="186"></td>
<td id="LC186" class="blob-code blob-code-inner js-file-line"> roiManager("Select", roiManager("Count")-2);</td>
</tr>
<tr>
<td id="L187" class="blob-num js-line-number js-code-nav-line-number" data-line-number="187"></td>
<td id="LC187" class="blob-code blob-code-inner js-file-line"> run("Enlarge...", "enlarge=" + radius);</td>
</tr>
<tr>
<td id="L188" class="blob-num js-line-number js-code-nav-line-number" data-line-number="188"></td>
<td id="LC188" class="blob-code blob-code-inner js-file-line"> Roi.setName("Centrosome_" + (j+1) + ": Circle_3");</td>
</tr>
<tr>
<td id="L189" class="blob-num js-line-number js-code-nav-line-number" data-line-number="189"></td>
<td id="LC189" class="blob-code blob-code-inner js-file-line"> roiManager("Add");</td>
</tr>
<tr>
<td id="L190" class="blob-num js-line-number js-code-nav-line-number" data-line-number="190"></td>
<td id="LC190" class="blob-code blob-code-inner js-file-line"> roiManager("Select", newArray(roiManager("Count")-3, roiManager("Count")-1));</td>
</tr>
<tr>
<td id="L191" class="blob-num js-line-number js-code-nav-line-number" data-line-number="191"></td>
<td id="LC191" class="blob-code blob-code-inner js-file-line"> roiManager("XOR");</td>
</tr>
<tr>
<td id="L192" class="blob-num js-line-number js-code-nav-line-number" data-line-number="192"></td>
<td id="LC192" class="blob-code blob-code-inner js-file-line"> Roi.setName("Centrosome_" + (j+1) + ": Band_3");</td>
</tr>
<tr>
<td id="L193" class="blob-num js-line-number js-code-nav-line-number" data-line-number="193"></td>
<td id="LC193" class="blob-code blob-code-inner js-file-line"> roiManager("Set Color", "orange");</td>
</tr>
<tr>
<td id="L194" class="blob-num js-line-number js-code-nav-line-number" data-line-number="194"></td>
<td id="LC194" class="blob-code blob-code-inner js-file-line"> roiManager("Add");</td>
</tr>
<tr>
<td id="L195" class="blob-num js-line-number js-code-nav-line-number" data-line-number="195"></td>
<td id="LC195" class="blob-code blob-code-inner js-file-line"> roiManager("Select", roiManager("Count")-1);</td>
</tr>
<tr>
<td id="L196" class="blob-num js-line-number js-code-nav-line-number" data-line-number="196"></td>
<td id="LC196" class="blob-code blob-code-inner js-file-line"> getStatistics(area, Band_Three[j], min, max, std, histogram);</td>
</tr>
<tr>
<td id="L197" class="blob-num js-line-number js-code-nav-line-number" data-line-number="197"></td>
<td id="LC197" class="blob-code blob-code-inner js-file-line">
</td>
</tr>
<tr>
<td id="L198" class="blob-num js-line-number js-code-nav-line-number" data-line-number="198"></td>
<td id="LC198" class="blob-code blob-code-inner js-file-line"> roiManager("Select", roiManager("Count")-2);</td>
</tr>
<tr>
<td id="L199" class="blob-num js-line-number js-code-nav-line-number" data-line-number="199"></td>
<td id="LC199" class="blob-code blob-code-inner js-file-line"> run("Enlarge...", "enlarge=" + radius);</td>
</tr>
<tr>
<td id="L200" class="blob-num js-line-number js-code-nav-line-number" data-line-number="200"></td>
<td id="LC200" class="blob-code blob-code-inner js-file-line"> Roi.setName("Centrosome_" + (j+1) + ": Circle_4");</td>
</tr>
<tr>
<td id="L201" class="blob-num js-line-number js-code-nav-line-number" data-line-number="201"></td>
<td id="LC201" class="blob-code blob-code-inner js-file-line"> roiManager("Add");</td>
</tr>
<tr>
<td id="L202" class="blob-num js-line-number js-code-nav-line-number" data-line-number="202"></td>
<td id="LC202" class="blob-code blob-code-inner js-file-line"> roiManager("Select", newArray(roiManager("Count")-3, roiManager("Count")-1));</td>
</tr>
<tr>
<td id="L203" class="blob-num js-line-number js-code-nav-line-number" data-line-number="203"></td>
<td id="LC203" class="blob-code blob-code-inner js-file-line"> roiManager("XOR");</td>
</tr>
<tr>
<td id="L204" class="blob-num js-line-number js-code-nav-line-number" data-line-number="204"></td>
<td id="LC204" class="blob-code blob-code-inner js-file-line"> Roi.setName("Centrosome_" + (j+1) + ": Band_4");</td>
</tr>
<tr>
<td id="L205" class="blob-num js-line-number js-code-nav-line-number" data-line-number="205"></td>
<td id="LC205" class="blob-code blob-code-inner js-file-line"> roiManager("Set Color", "orange");</td>
</tr>
<tr>
<td id="L206" class="blob-num js-line-number js-code-nav-line-number" data-line-number="206"></td>
<td id="LC206" class="blob-code blob-code-inner js-file-line"> roiManager("Add");</td>
</tr>
<tr>
<td id="L207" class="blob-num js-line-number js-code-nav-line-number" data-line-number="207"></td>
<td id="LC207" class="blob-code blob-code-inner js-file-line"> roiManager("Select", roiManager("Count")-1);</td>
</tr>
<tr>
<td id="L208" class="blob-num js-line-number js-code-nav-line-number" data-line-number="208"></td>
<td id="LC208" class="blob-code blob-code-inner js-file-line"> getStatistics(area, Band_Four[j], min, max, std, histogram);</td>
</tr>
<tr>
<td id="L209" class="blob-num js-line-number js-code-nav-line-number" data-line-number="209"></td>
<td id="LC209" class="blob-code blob-code-inner js-file-line">
</td>
</tr>
<tr>
<td id="L210" class="blob-num js-line-number js-code-nav-line-number" data-line-number="210"></td>
<td id="LC210" class="blob-code blob-code-inner js-file-line"> roiManager("Select", roiManager("Count")-2);</td>
</tr>
<tr>
<td id="L211" class="blob-num js-line-number js-code-nav-line-number" data-line-number="211"></td>
<td id="LC211" class="blob-code blob-code-inner js-file-line"> run("Enlarge...", "enlarge=" + radius);</td>
</tr>
<tr>
<td id="L212" class="blob-num js-line-number js-code-nav-line-number" data-line-number="212"></td>
<td id="LC212" class="blob-code blob-code-inner js-file-line"> Roi.setName("Centrosome_" + (j+1) + ": Circle_5");</td>
</tr>
<tr>
<td id="L213" class="blob-num js-line-number js-code-nav-line-number" data-line-number="213"></td>
<td id="LC213" class="blob-code blob-code-inner js-file-line"> roiManager("Add");</td>
</tr>
<tr>
<td id="L214" class="blob-num js-line-number js-code-nav-line-number" data-line-number="214"></td>
<td id="LC214" class="blob-code blob-code-inner js-file-line"> roiManager("Select", newArray(roiManager("Count")-3, roiManager("Count")-1));</td>
</tr>
<tr>
<td id="L215" class="blob-num js-line-number js-code-nav-line-number" data-line-number="215"></td>
<td id="LC215" class="blob-code blob-code-inner js-file-line"> roiManager("XOR");</td>
</tr>
<tr>
<td id="L216" class="blob-num js-line-number js-code-nav-line-number" data-line-number="216"></td>
<td id="LC216" class="blob-code blob-code-inner js-file-line"> Roi.setName("Centrosome_" + (j+1) + ": Band_5");</td>
</tr>
<tr>
<td id="L217" class="blob-num js-line-number js-code-nav-line-number" data-line-number="217"></td>
<td id="LC217" class="blob-code blob-code-inner js-file-line"> roiManager("Set Color", "orange");</td>
</tr>
<tr>
<td id="L218" class="blob-num js-line-number js-code-nav-line-number" data-line-number="218"></td>
<td id="LC218" class="blob-code blob-code-inner js-file-line"> roiManager("Add");</td>
</tr>
<tr>
<td id="L219" class="blob-num js-line-number js-code-nav-line-number" data-line-number="219"></td>
<td id="LC219" class="blob-code blob-code-inner js-file-line"> roiManager("Select", roiManager("Count")-1);</td>
</tr>
<tr>
<td id="L220" class="blob-num js-line-number js-code-nav-line-number" data-line-number="220"></td>
<td id="LC220" class="blob-code blob-code-inner js-file-line"> getStatistics(area, Band_Five[j], min, max, std, histogram);</td>
</tr>
<tr>
<td id="L221" class="blob-num js-line-number js-code-nav-line-number" data-line-number="221"></td>
<td id="LC221" class="blob-code blob-code-inner js-file-line"> }</td>
</tr>
<tr>
<td id="L222" class="blob-num js-line-number js-code-nav-line-number" data-line-number="222"></td>
<td id="LC222" class="blob-code blob-code-inner js-file-line">
</td>
</tr>
<tr>
<td id="L223" class="blob-num js-line-number js-code-nav-line-number" data-line-number="223"></td>
<td id="LC223" class="blob-code blob-code-inner js-file-line"> // -- Save image with all ROIs - think about the ones that are over the edge</td>
</tr>
<tr>
<td id="L224" class="blob-num js-line-number js-code-nav-line-number" data-line-number="224"></td>
<td id="LC224" class="blob-code blob-code-inner js-file-line"> selectWindow("MProjection");</td>
</tr>
<tr>
<td id="L225" class="blob-num js-line-number js-code-nav-line-number" data-line-number="225"></td>
<td id="LC225" class="blob-code blob-code-inner js-file-line"> Stack.setChannel(1);</td>
</tr>
<tr>
<td id="L226" class="blob-num js-line-number js-code-nav-line-number" data-line-number="226"></td>
<td id="LC226" class="blob-code blob-code-inner js-file-line"> run("Enhance Contrast...", "saturated=0.3 normalize");</td>
</tr>
<tr>
<td id="L227" class="blob-num js-line-number js-code-nav-line-number" data-line-number="227"></td>
<td id="LC227" class="blob-code blob-code-inner js-file-line"> Stack.setChannel(2);</td>
</tr>
<tr>
<td id="L228" class="blob-num js-line-number js-code-nav-line-number" data-line-number="228"></td>
<td id="LC228" class="blob-code blob-code-inner js-file-line"> run("Enhance Contrast...", "saturated=0.3 normalize");</td>
</tr>
<tr>
<td id="L229" class="blob-num js-line-number js-code-nav-line-number" data-line-number="229"></td>
<td id="LC229" class="blob-code blob-code-inner js-file-line"> Stack.setChannel(3);</td>
</tr>
<tr>
<td id="L230" class="blob-num js-line-number js-code-nav-line-number" data-line-number="230"></td>
<td id="LC230" class="blob-code blob-code-inner js-file-line"> run("Enhance Contrast...", "saturated=0.3 normalize");</td>
</tr>
<tr>
<td id="L231" class="blob-num js-line-number js-code-nav-line-number" data-line-number="231"></td>
<td id="LC231" class="blob-code blob-code-inner js-file-line"> run("RGB Color");</td>
</tr>
<tr>
<td id="L232" class="blob-num js-line-number js-code-nav-line-number" data-line-number="232"></td>
<td id="LC232" class="blob-code blob-code-inner js-file-line"> roiManager("Show All without labels");</td>
</tr>
<tr>
<td id="L233" class="blob-num js-line-number js-code-nav-line-number" data-line-number="233"></td>
<td id="LC233" class="blob-code blob-code-inner js-file-line"> roiManager("Save", outputFolder + File.separator + imgName + "_ROIset.zip");</td>
</tr>
<tr>
<td id="L234" class="blob-num js-line-number js-code-nav-line-number" data-line-number="234"></td>
<td id="LC234" class="blob-code blob-code-inner js-file-line"> run("Flatten");</td>
</tr>
<tr>
<td id="L235" class="blob-num js-line-number js-code-nav-line-number" data-line-number="235"></td>
<td id="LC235" class="blob-code blob-code-inner js-file-line"> saveAs("Tiff", outputFolder + File.separator + imgName + "_Outlines.tif");</td>
</tr>
<tr>
<td id="L236" class="blob-num js-line-number js-code-nav-line-number" data-line-number="236"></td>
<td id="LC236" class="blob-code blob-code-inner js-file-line">
</td>
</tr>
<tr>
<td id="L237" class="blob-num js-line-number js-code-nav-line-number" data-line-number="237"></td>
<td id="LC237" class="blob-code blob-code-inner js-file-line"> run("Close All");</td>
</tr>
<tr>
<td id="L238" class="blob-num js-line-number js-code-nav-line-number" data-line-number="238"></td>
<td id="LC238" class="blob-code blob-code-inner js-file-line"> roiManager("Reset");</td>
</tr>
<tr>
<td id="L239" class="blob-num js-line-number js-code-nav-line-number" data-line-number="239"></td>
<td id="LC239" class="blob-code blob-code-inner js-file-line">
</td>
</tr>
<tr>
<td id="L240" class="blob-num js-line-number js-code-nav-line-number" data-line-number="240"></td>
<td id="LC240" class="blob-code blob-code-inner js-file-line"> // -- Save the results per image</td>
</tr>
<tr>
<td id="L241" class="blob-num js-line-number js-code-nav-line-number" data-line-number="241"></td>
<td id="LC241" class="blob-code blob-code-inner js-file-line"> Array.show("Mean Intensity", Label, Centrosome, Band_One, Band_Two, Band_Three, Band_Four, Band_Five);</td>
</tr>
<tr>
<td id="L242" class="blob-num js-line-number js-code-nav-line-number" data-line-number="242"></td>
<td id="LC242" class="blob-code blob-code-inner js-file-line"> saveAs("Results", outputFolder + File.separator + imgName + "_Results.csv");</td>
</tr>
<tr>
<td id="L243" class="blob-num js-line-number js-code-nav-line-number" data-line-number="243"></td>
<td id="LC243" class="blob-code blob-code-inner js-file-line"> run("Close");</td>
</tr>
<tr>
<td id="L244" class="blob-num js-line-number js-code-nav-line-number" data-line-number="244"></td>
<td id="LC244" class="blob-code blob-code-inner js-file-line">
</td>
</tr>
<tr>
<td id="L245" class="blob-num js-line-number js-code-nav-line-number" data-line-number="245"></td>
<td id="LC245" class="blob-code blob-code-inner js-file-line"> // -- Take means per image to save for overall mean results</td>
</tr>
<tr>
<td id="L246" class="blob-num js-line-number js-code-nav-line-number" data-line-number="246"></td>
<td id="LC246" class="blob-code blob-code-inner js-file-line"> Array.getStatistics(Centrosome, min, max, Centrosome_Mean[i], stdDev);</td>
</tr>
<tr>
<td id="L247" class="blob-num js-line-number js-code-nav-line-number" data-line-number="247"></td>
<td id="LC247" class="blob-code blob-code-inner js-file-line"> Array.getStatistics(Band_One, min, max, Band_One_Mean[i], stdDev);</td>
</tr>
<tr>
<td id="L248" class="blob-num js-line-number js-code-nav-line-number" data-line-number="248"></td>
<td id="LC248" class="blob-code blob-code-inner js-file-line"> Array.getStatistics(Band_Two, min, max, Band_Two_Mean[i], stdDev);</td>
</tr>
<tr>
<td id="L249" class="blob-num js-line-number js-code-nav-line-number" data-line-number="249"></td>
<td id="LC249" class="blob-code blob-code-inner js-file-line"> Array.getStatistics(Band_Three, min, max, Band_Three_Mean[i], stdDev);</td>
</tr>
<tr>
<td id="L250" class="blob-num js-line-number js-code-nav-line-number" data-line-number="250"></td>
<td id="LC250" class="blob-code blob-code-inner js-file-line"> Array.getStatistics(Band_Four, min, max, Band_Four_Mean[i], stdDev);</td>
</tr>
<tr>
<td id="L251" class="blob-num js-line-number js-code-nav-line-number" data-line-number="251"></td>
<td id="LC251" class="blob-code blob-code-inner js-file-line"> Array.getStatistics(Band_Five, min, max, Band_Five_Mean[i], stdDev); </td>
</tr>
<tr>
<td id="L252" class="blob-num js-line-number js-code-nav-line-number" data-line-number="252"></td>
<td id="LC252" class="blob-code blob-code-inner js-file-line"> </td>
</tr>
<tr>
<td id="L253" class="blob-num js-line-number js-code-nav-line-number" data-line-number="253"></td>
<td id="LC253" class="blob-code blob-code-inner js-file-line">}</td>
</tr>
<tr>
<td id="L254" class="blob-num js-line-number js-code-nav-line-number" data-line-number="254"></td>
<td id="LC254" class="blob-code blob-code-inner js-file-line">
</td>
</tr>
<tr>
<td id="L255" class="blob-num js-line-number js-code-nav-line-number" data-line-number="255"></td>
<td id="LC255" class="blob-code blob-code-inner js-file-line">//--------------------------------//-----------------------------------------------------------------------------------</td>
</tr>
<tr>
<td id="L256" class="blob-num js-line-number js-code-nav-line-number" data-line-number="256"></td>
<td id="LC256" class="blob-code blob-code-inner js-file-line">//-- Part 5: Closing loop and finishing off</td>
</tr>
<tr>
<td id="L257" class="blob-num js-line-number js-code-nav-line-number" data-line-number="257"></td>
<td id="LC257" class="blob-code blob-code-inner js-file-line">//--------------------------------//-----------------------------------------------------------------------------------</td>
</tr>
<tr>
<td id="L258" class="blob-num js-line-number js-code-nav-line-number" data-line-number="258"></td>
<td id="LC258" class="blob-code blob-code-inner js-file-line">
</td>
</tr>
<tr>
<td id="L259" class="blob-num js-line-number js-code-nav-line-number" data-line-number="259"></td>
<td id="LC259" class="blob-code blob-code-inner js-file-line">// -- Save the average results for each image</td>
</tr>
<tr>
<td id="L260" class="blob-num js-line-number js-code-nav-line-number" data-line-number="260"></td>
<td id="LC260" class="blob-code blob-code-inner js-file-line">Array.show("Mean Intensity", Filename , Signal_Mean, Centrosome_Mean, Band_One_Mean, Band_Two_Mean, Band_Three_Mean, Band_Four_Mean, Band_Five_Mean );</td>
</tr>
<tr>
<td id="L261" class="blob-num js-line-number js-code-nav-line-number" data-line-number="261"></td>
<td id="LC261" class="blob-code blob-code-inner js-file-line">saveAs("Results", outputFolder + File.separator + "Mean intensity for centrosomes bands per image.csv");</td>
</tr>
<tr>
<td id="L262" class="blob-num js-line-number js-code-nav-line-number" data-line-number="262"></td>
<td id="LC262" class="blob-code blob-code-inner js-file-line">run("Close");</td>
</tr>
<tr>
<td id="L263" class="blob-num js-line-number js-code-nav-line-number" data-line-number="263"></td>
<td id="LC263" class="blob-code blob-code-inner js-file-line">
</td>
</tr>
<tr>
<td id="L264" class="blob-num js-line-number js-code-nav-line-number" data-line-number="264"></td>
<td id="LC264" class="blob-code blob-code-inner js-file-line">run("Collect Garbage");</td>
</tr>
<tr>
<td id="L265" class="blob-num js-line-number js-code-nav-line-number" data-line-number="265"></td>
<td id="LC265" class="blob-code blob-code-inner js-file-line">
</td>
</tr>
<tr>
<td id="L266" class="blob-num js-line-number js-code-nav-line-number" data-line-number="266"></td>
<td id="LC266" class="blob-code blob-code-inner js-file-line">getDateAndTime(year, month, dayOfWeek, dayOfMonth, hour, minute, second, msec);</td>
</tr>
<tr>
<td id="L267" class="blob-num js-line-number js-code-nav-line-number" data-line-number="267"></td>
<td id="LC267" class="blob-code blob-code-inner js-file-line">print("This macro was run on " + dayOfMonth + "/" + month+1 + "/" + year + ": " + hour + ":" + minute + "\nUsing a radius of " + radius + " " + unit + "\nOn " + projection + " projections");</td>
</tr>
<tr>
<td id="L268" class="blob-num js-line-number js-code-nav-line-number" data-line-number="268"></td>
<td id="LC268" class="blob-code blob-code-inner js-file-line">
</td>
</tr>
<tr>
<td id="L269" class="blob-num js-line-number js-code-nav-line-number" data-line-number="269"></td>
<td id="LC269" class="blob-code blob-code-inner js-file-line">selectWindow("Log");</td>
</tr>
<tr>
<td id="L270" class="blob-num js-line-number js-code-nav-line-number" data-line-number="270"></td>
<td id="LC270" class="blob-code blob-code-inner js-file-line">saveAs("Text", outputFolder + "Details of macro run");</td>
</tr>
<tr>
<td id="L271" class="blob-num js-line-number js-code-nav-line-number" data-line-number="271"></td>
<td id="LC271" class="blob-code blob-code-inner js-file-line">print("\\Clear");</td>
</tr>
<tr>
<td id="L272" class="blob-num js-line-number js-code-nav-line-number" data-line-number="272"></td>
<td id="LC272" class="blob-code blob-code-inner js-file-line">
</td>
</tr>
<tr>
<td id="L273" class="blob-num js-line-number js-code-nav-line-number" data-line-number="273"></td>
<td id="LC273" class="blob-code blob-code-inner js-file-line">Dialog.create("Progress");</td>
</tr>
<tr>
<td id="L274" class="blob-num js-line-number js-code-nav-line-number" data-line-number="274"></td>
<td id="LC274" class="blob-code blob-code-inner js-file-line">Dialog.addMessage("Macro Complete!");</td>
</tr>
<tr>
<td id="L275" class="blob-num js-line-number js-code-nav-line-number" data-line-number="275"></td>
<td id="LC275" class="blob-code blob-code-inner js-file-line">Dialog.show;</td>
</tr>
<tr>
<td id="L276" class="blob-num js-line-number js-code-nav-line-number" data-line-number="276"></td>
<td id="LC276" class="blob-code blob-code-inner js-file-line">
</td>
</tr>
<tr>
<td id="L277" class="blob-num js-line-number js-code-nav-line-number" data-line-number="277"></td>
<td id="LC277" class="blob-code blob-code-inner js-file-line">//--------------------------------//-----------------------------------------------------------------------------------</td>
</tr>
<tr>
<td id="L278" class="blob-num js-line-number js-code-nav-line-number" data-line-number="278"></td>
<td id="LC278" class="blob-code blob-code-inner js-file-line">//-- Epilogue: Functions</td>
</tr>
<tr>
<td id="L279" class="blob-num js-line-number js-code-nav-line-number" data-line-number="279"></td>
<td id="LC279" class="blob-code blob-code-inner js-file-line">//--------------------------------//-----------------------------------------------------------------------------------</td>
</tr>
<tr>
<td id="L280" class="blob-num js-line-number js-code-nav-line-number" data-line-number="280"></td>
<td id="LC280" class="blob-code blob-code-inner js-file-line">
</td>
</tr>
<tr>
<td id="L281" class="blob-num js-line-number js-code-nav-line-number" data-line-number="281"></td>
<td id="LC281" class="blob-code blob-code-inner js-file-line">function getFileTree(dir , fileTree){</td>
</tr>
<tr>
<td id="L282" class="blob-num js-line-number js-code-nav-line-number" data-line-number="282"></td>
<td id="LC282" class="blob-code blob-code-inner js-file-line"> list = getFileList(dir);</td>
</tr>
<tr>
<td id="L283" class="blob-num js-line-number js-code-nav-line-number" data-line-number="283"></td>
<td id="LC283" class="blob-code blob-code-inner js-file-line">
</td>
</tr>
<tr>
<td id="L284" class="blob-num js-line-number js-code-nav-line-number" data-line-number="284"></td>
<td id="LC284" class="blob-code blob-code-inner js-file-line"> for(f = 0; f < list.length; f++){</td>
</tr>
<tr>
<td id="L285" class="blob-num js-line-number js-code-nav-line-number" data-line-number="285"></td>
<td id="LC285" class="blob-code blob-code-inner js-file-line"> if (matches(list[f], "(?i).*\\.(tif|tiff|nd2|ims|oib)$"))</td>
</tr>
<tr>
<td id="L286" class="blob-num js-line-number js-code-nav-line-number" data-line-number="286"></td>
<td id="LC286" class="blob-code blob-code-inner js-file-line"> fileTree = Array.concat(fileTree, dir + list[f]);</td>
</tr>
<tr>
<td id="L287" class="blob-num js-line-number js-code-nav-line-number" data-line-number="287"></td>
<td id="LC287" class="blob-code blob-code-inner js-file-line"> if(File.isDirectory(dir + File.separator + list[f]))</td>
</tr>
<tr>
<td id="L288" class="blob-num js-line-number js-code-nav-line-number" data-line-number="288"></td>
<td id="LC288" class="blob-code blob-code-inner js-file-line"> fileTree = getFileTree(dir + list[f],fileTree);</td>
</tr>
<tr>
<td id="L289" class="blob-num js-line-number js-code-nav-line-number" data-line-number="289"></td>
<td id="LC289" class="blob-code blob-code-inner js-file-line"> }</td>
</tr>
<tr>
<td id="L290" class="blob-num js-line-number js-code-nav-line-number" data-line-number="290"></td>
<td id="LC290" class="blob-code blob-code-inner js-file-line"> return fileTree;</td>
</tr>
<tr>
<td id="L291" class="blob-num js-line-number js-code-nav-line-number" data-line-number="291"></td>
<td id="LC291" class="blob-code blob-code-inner js-file-line">}</td>
</tr>
</table>
</div>
<details class="details-reset details-overlay BlobToolbar position-absolute js-file-line-actions dropdown d-none" aria-hidden="true">
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<svg aria-hidden="true" height="16" viewBox="0 0 16 16" version="1.1" width="16" data-view-component="true" class="octicon octicon-kebab-horizontal">
<path d="M8 9a1.5 1.5 0 100-3 1.5 1.5 0 000 3zM1.5 9a1.5 1.5 0 100-3 1.5 1.5 0 000 3zm13 0a1.5 1.5 0 100-3 1.5 1.5 0 000 3z"></path>
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Copy permalink
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<summary data-hotkey="l" aria-label="Jump to line"></summary>
<details-dialog class="Box Box--overlay d-flex flex-column anim-fade-in fast linejump" aria-label="Jump to line">
<!-- '"` --><!-- </textarea></xmp> --></option></form><form class="js-jump-to-line-form Box-body d-flex" action="" accept-charset="UTF-8" method="get">
<input class="form-control flex-auto mr-3 linejump-input js-jump-to-line-field" type="text" placeholder="Jump to line…" aria-label="Jump to line" autofocus>
<button data-close-dialog="" type="submit" data-view-component="true" class="btn"> Go
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