2016.12.16

2016.12.16

Contributors: Chris Barnes, Andrew Champion, Tom Kazimiers

Notes

• Virtual env update required
• Postgres 9.6 is now supported.

Features and enhancements

3D Viewer:

• Shift+Click can now be used to jump to arbitrary locations on rendered skeletons. Objects already clickable in the past (like tags or the soma spheres) are still given precedence.

Tag Table:

• New widget allowing users to get information about node label usage in the project, and select skeletons based on labels which their nodes have.
• Accessible with Ctrl+Space by the name 'tag-table' or through the 'T' widget button in the Tracing Tool.

Measurement Table:

• The neuron name is now quoted in the CSV file export. This makes it more robust when commas are used in the name representation (e.g. if annotations).
• XLSX spreadsheet export is now supported through an "Export XLSX" button.

Importer:

• Add support for importing ontology and classification information along with projects, stacks and stack groups in project file based import ("Image data importer" in admin view).
• Projects to be imported can be split across multiple documents, if local or remote file import is used. This helps organizing image collections manually.

Tracing tool:

• Holding P will show the active skeleton in all open 3D viewers.
• The semicolon (";") key no longer switches to skeleton tracing mode, because it is active by default.
• Bookmarks can be set by pressing semicolon (";") and then a marker key, which will mark the active node (or location if no node is active) with that key. Pressing backtick ("`") followed by the marker key will return to the marked node or location. Pressing single quote ("'") followed by the marker key will instead activate the marked skeleton and move to the closest skeleton node.
• Shift + H will go to the last node you edited in any skeleton.

Tracing layer:

• Connectors connected to the active skeleton are now colored with a distinct, more yellow hue of orange, even if the connection is not in the visible section.

Miscellaneous:

• The Graph Widget can handle larger graphs much better now. Also its mouse action have slightly changed: moving while having the left mouse button down will pan the view, pressing additionally the Ctrl key enters rectangular selection mode.

Deprecations and Removals

• Special behavior of tile source type 2 stacks to interoperate with a Volumina tile server prototype has been removed.

Bug fixes

• Review widget: auto centering works again
• Review widget: location lookup of warnings now works again in all cases.
• Skeleton source subscriptions: fix accidental sharing of skeleton sources. This caused e.g. losing the connection between a Selection Table and a 3D viewer as soon as another 3D viewer was opened.
• The Classification Editor of CATMAID's Ontology Tool can be started again.
• Using the closing bracket ("]") to walk a neuron does not stop working anymore after the end of a branch is reached.
• 3D viewer: finding the date of the most recent change among all skeletons considered in a history animation now works as expected. The end point of the animation is now calculated correctly and all changes can be seen.
• The Classification Clustering Widget can be opened again.

API Changes

Additions

• GET /{project_id}/labels/stats
  Get statistics on node label usage for the project.
• POST /{project_id}/skeletons/node-labels
  Return mappings from node label IDs to IDs of skeletons which include
  a node with that label.

Modifications

None.

Deprecations

None.

Removals

None.