https://github.com/catmaid/CATMAID
Release 2017.12.07 created by Tom Kazimiers on 07 December 2017, 05:30:27 UTC
2017.12.07
========== Contributors: Albert Cardona, Andrew Champion, Chris Barnes, Tom Kazimiers Notes ----- - PostgreSQL 9.6 and Postgis 2.4 are now required. - A virtualenv update is required. - New settings field: CROPPING_VERIFY_CERTIFICATES. This controls whether SSL certificates should be verified during cropping and defaults to True. - The NODE_LIST_MAXIMUM_COUNT setting can now be set to None, which disables node limiting. If node count limiting isn't really needed in most cases, this can slighly improve query performance. - The file `UPDATE.md` will now list all administration related changes for each release, including required manual tasks. These changes also continue to be part of this change log. - Requires running of: manage.py catmaid_update_project_configuration - Tracing data is now by default transmitted in a binary form, please make therefore sure your web-server applies GZIP not only to the "application/json" content type, but also to "application/octet-stream". For Nginx this would be the gzip_types setting. Features and enhancements ------------------------- Node filters: - A new node filter called "In skeleton source" has been added. This allows to add a filter which only allows nodes of a particular set of skeletons, accessed through a skeleton source. This can be useful to look at connectivity of a particular set of neurons. It can of course be combined with other filters like volume intersection. - New filter: Pruned arbor, which keeps the arbor proximal to the (tagged) cut points, discarding distal subarbors. Connector table: - Node filters are now supported. - Attachment connectors are now supported. 3D viewer: - Landmarks and landmark groups can be displayed. Similarly to volumes individual groups can be selected and adjusted through the "View settings" tab. Apart from the color and mesh-faces option for groups, it is possible to scale landmarks. - All visible skeletons can now be exported as Wavefront OBJ file. Each skeleton will be rendered as a separate group, colors are preserved and written out as material file (MTL). Both files can be compressed as ZIP file on the fly and it is possible to generate a simple line based export as well as a mesh based representation using a user definable radius. The generated ZIP file can be used with services like augment.com. Neuron history widget: - A user filter can now be applied through the respective checkbox drop down element. If at least one user is selected, only events caused by those users are respected. New connector types: - Two new connector relations are available: attached_to and close_to. Like other connector relations, they can be used to link treenodes to connectors and can be used with the help of Alt + Click context menu when a treenode is selected. They are available as "Attachment" and "Close to". - If If a connector has at least one attachment relation is viewed as "Attachment connector" and additional clicks with such a connector selected will create "Close to" edges. - To add more information about the nature of an attachment, the connector should be labeled, e.g. as "vesicle". Connectivity Widget: - All skeletons linked through a attached_to -> connector -> close_to relationship are now shown in a separate table if the "Show attachments" option is enabled. Export management command: - The export management command will now also export meta-annotations when the --annotation option is set. All meta-annotations of annotations directly linked to the exported neurons are exported, too. - Users referenced by any of the exported objects are now also exported automatically. This can be disabled using the --nousers options. - User references are now stored as usernames rather than numerical IDs. This removes the requirement of always also exporting user models, because users can be mapped based on their usernames. Import management command: - The new --map-users option allows to map users referenced in the imported data to already existing users in the database. This makes updating existing databases easier and removes the de facto import data requirement to contain user models. By default --map-users is not set. - The new --create-unknown-users option will instruct the importer to create new inactive user accounts for users that aren't included as objects in the imported data. If user mapping is enabled, accounts would only be created for users that can't be mapped and are also not included in the import data. By default --create-unknown-users is not set. - Imported class, class instance and relation objects are skipped when existing objects in the target project have the same name. This makes merging of projects also possible for semantic data (e.g. annotations, tags). The only exception are neuron class instances, where two different objects are allowed to have the same name. - The importer now won't keep the IDs from spatial objects in the input source, but will instead always create new objects. This ensures no existing data is replaced and allows importing different sources into a single CATMAID instance. If the original IDs have to be used, the ``--preserve-ids`` option can be used. This is done for treenodes, connects, and their links. Miscellaneous: - Users can now choose alternative markers for connector nodes, which do not obscure the object being annotated: this encourages manually annotating synapses etc. in a manner which is more comparable with automated detections - Exported sub-stacks now include the Z resolution. - Added table of reviewers vs number of nodes reviewed to the "Summary Info" in the Selection Table widget. - Synapse distribution plot: global and single-axis zoom and pan are now supported. - Neuron dendrogram: nodes linked to connectors (synaptic sites) can now be highlighted. - Tracing layer: cached tracing data is now used by default when showing sub-views of previously loaded data. This is useful for e.g. quickly zooming in. Like with the regular node cache, views not used for one minute will be thrown away. - All users can now view their user analytics plot with the help of the Project Statistics widget. - The NRRD file export can now transform from FAFB v14 into template brain space. - Synapse Fractions: the button "Group all ungrouped" will move all skeletons that are not part of a group already and not part of "others" into a new group. To also include skeletons in "others", use a synapse threshold of zero in the "Filter partners" tab. - Selection Table: Open/Save (JSON) does now preserve the order of skeletons. - Tracing data should load faster due to spatial query improvements and reduction of transferred data. The tracing layer transfers data now in binary by default, which can be adjusted in through the tracing layer settings. - The catmaid_setup_tracing_for_project management command does not require a --user argument anymore. If not provided, the first available admin user will be used. Bug fixes --------- - 3D Viewer: the visibility of skeletons with connector colors the same as the skeleton can now be controlled correctly. - Selecting nodes explicitly with multiple stackviewers open (e.g. by Shift-Click in the 3D Viewer) sometimes raised an error about not being able to find the selected node. This is fixed now. - Entries in the Treenode Table can now be correctly sorted by date. - Cropping tasks can now work with HTTPS URLs. - Graph widget: new skeletons can now be added again after individual skeletons have been split. API changes ----------- Additions --------- - `POST /{project_id}/nodes/location`: Get the location of multiple nodes, expects a `node_ids` parameter. - `GET /{project_id}/connectors/` now provides a new API to query connectors directly and not only links. The previous API is available as `GET /{project_id}/connctors/links/` (see below). - `GET /{project_id}/skeletons/{skeleton_id}/neuroglancer`: Export a morphology-only skeleton in neuroglancer's binary format. Modifications ------------- - `GET /{project_id}/connector/user-info` has been replaced with `GET /{project_id}/connectors/user-info`. Functionality is the same. - `GET /{project_id}/connectors/` has been replaced with `GET /{project_if}/connectors/links/`. Functionality is the same. - `POST /{project_id}/node/list` offers a new optional parameter "format", which is set by default to 'json', but can be set to 'msgpack' to use msgpack binary encoding of the result. Deprecations ------------ None. Removals -------- None.
Target: 63e464f76cba970b5a018af9a31be5ab20880e2a
Directory: 0484221e33396576f8273af916d3c202a384c81e
Directory: 0484221e33396576f8273af916d3c202a384c81e
