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                 This section is for MAC (using Terminal commands).
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Install Xcode
-------------

  xcode-select --install

Check:
  xcode-select --version
  git --version

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Install HomeBrew
----------------

  /bin/bash -c "$(curl -fsSL https://raw.githubusercontent.com/Homebrew/install/master/install.sh)"

Check:
  brew --version

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Install NodeJS
--------------

  brew install node
  
Check:
  node -v
  npm -v  

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Install ffmpeg
--------------

  brew install ffmpeg
  
Check:
  ffmpeg 

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Install Python3
---------------

 brew install python3

Check:
  python3 --version
  pip3 --version

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Install python packages
-----------------------

  pip3 install numpy scipy matplotlib
  pip3 install scikit-image scikit-learn
  pip3 install jupyterlab ipywidgets ipyfilechooser ipympl

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Install JupyterLab extension
----------------------------

  jupyter labextension install @jupyter-widgets/jupyterlab-manager
  jupyter labextension install jupyter-matplotlib
  jupyter nbextension enable --py widgetsnbextension 

Check:
  jupyter labextension list

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Install Fiji ImageJ
-------------------

  Download and install: https://imagej.net/Fiji/Downloads
  
Check:
  launch the Fiji application 

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Download the cell_tools project from github
-------------------------------------------

  git clone https://github.com/jrugis/cell_tools.git

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Use Fiji to convert oir files to tif's
--------------------------------------

Copy oir files to folder: cell_tools/IMAGING/image_stacks/ 

  Within Fiji, run macro: cell_tools/IMAGING/image_stacks/oir2tif.ijm

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Launch Notebook
---------------
 
  jupyter-lab
    Navigate to and launch the notebook: roi_identification.ipynb

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Update project notebook to latest version
-----------------------------------------

Navigate into your cell_tools folder, then...
  git fetch origin
  git reset --hard origin/master
  
NOTE: This operation will leave your results folder intact, but
      will overwrite any changes that you made in your copy of 
      the notebook !!!!!! 


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                 This section is for PC.
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Install git
-----------

  Download and execute installer: https://git-scm.com/download/win
    default editor: Nano
    credential helper: none
  
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Install Anaconda
----------------

  Download and install: https://www.anaconda.com/products/individual
      
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Set Anaconda environments
-------------------------

Anaconda Navigator | Environments | Not installed
    install: ffmpeg, ipympl, nodejs 

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Install python packages
-----------------------

  Anaconda Navigator | Home | CMD.exe Prompt
	pip install ipywidgets
	pip install ipyfilechooser

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Install JupyterLab extension
----------------------------

  Anaconda Navigator | Home | CMD.exe Prompt
    jupyter lab build
    jupyter labextension install @jupyter-widgets/jupyterlab-manager
    jupyter labextension install jupyter-matplotlib
    jupyter nbextension enable --py widgetsnbextension 

Check:
  jupyter labextension list
	
********************************************************

Install Fiji ImageJ
-------------------

  Download and install: https://imagej.net/Fiji/Downloads
  
Check:
  launch the Fiji application 

********************************************************

Download the cell_tools project from github
-------------------------------------------

  Anaconda Navigator | Home | CMD.exe Prompt
    Navigate to where you want the project to go, then...
      git clone https://github.com/jrugis/cell_tools.git

********************************************************

Use Fiji to convert oir files to tif's
--------------------------------------

Copy oir files to folder: cell_tools/IMAGING/image_stacks/ 

  Within Fiji, run macro: cell_tools/IMAGING/image_stacks/oir2tif.ijm

********************************************************

Launch Notebook
---------------
 
Anaconda Navigator | Home | CMD.exe Prompt
  jupyter-lab
    Navigate to and launch the notebook: roi_identification.ipynb

********************************************************

Update project notebook to latest version
-----------------------------------------

Anaconda Navigator | Home | CMD.exe Prompt
  Navigate into your cell_tools folder, then...
    git fetch origin
    git reset --hard origin/master
  
NOTE: This operation will leave your results folder intact, but
      will overwrite any changes that you made in your copy of 
      the notebook !!!!!! 

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