Release 2017.01.19 · catmaid/CATMAID

2017.01.19

Contributors: Chris Barnes, Andrew Champion, Tom Kazimiers

The h5py dependency has been removed. If tile source tile 3 should be used in
a new instance, the h5py library has to be installed manually.

Connector Viewer:

A new tool used to view the connectors associated with a skeleton set
of skeletons.
Shows a grid of mini stack viewers with their own tracing overlays,
focused on connectors associated with the skeleton by a user-selected
relation (i.e. outgoing, incoming, gap junction or other).
Connectors can be sorted by their absolute or proportional depth on
their respective skeleton trees, by the connector ID or by the
skeleton name.
Mini stack viewers can inherit settings from a user-defined main stack
viewer; users can focus the main stack viewer on any connector by
clicking on its ID in the mini stack viewer title bar.
Users can open a connector table from a connector viewer and vice
versa.
Accessible with Ctrl+Space 'connector-viewer'.

Connectivity table:

Original colors of skeletons added to a Connectivity Table can now optionally
be used when using its skeletons in other widgets (new checkbox: "Original
color").
The colors used in the Connectivity Graph Plot are now the ones assigned to the
input skeletons, i.e. the ones selected in the Connectivity Widget. These in
turn are either its input skeleton color or the default skeleton color.
Manual re-ordering of partner count columns has been removed. Neurons can now
be re re-ordered through the list at the top with the help of two icons in
each row (up and down).
All partner tables are now paginated with a default page size of 50 entries.
The page size can be adjusted for all tables at the same time with a drop-down
menu at the top. "Select all" check-boxes select all entries across all pages.

Graph widget:

Active Graph Widget windows will now zoom in smaller steps if the Shift key
is pressed.
Graphs saved to a JSON file now keep visibility information. Loading them
will load all nodes hidden that have been hidden when saving the file
initially..

3D Viewer

Meshes are replaced with volumes and the "Show meshes" checkbox has been
removed. Existing meshes have been transformed into volumes.
The new coloring mode "Last Reviewer" will color skeleton nodes by the user
color of the user that reviewed them last. The "User colormap" button can be
used to show the mapping from color to user name.

Miscellaneous:

The Selection Table can now be opened through Ctrl+Space by using the handle
'selection-table' instead of 'neuron-staging-area'.
Project and stack menu entries are now sorted by default, which makes it easier
to deal with many projects and stacks.
Node bookmarks can now be removed through an X icon in their respective row in
the bookmark dialog.
Skeleton Analytics in the Review Widget will now identify nodes in broken
sections of all stacks linked to the current project.
The front page project list can now be loaded as a widget using Ctrl-Space
with 'project-list'.
Synaptic fractions: colors of groups and partners can now be changed through
legend of graph.
The tag table now has a refresh button to manually update the cache and
redraw the table.
The tag table can now open a treenode table pre-filtered for nodes with
the selected labels.

The size of the embedded 3D viewer in the split/merge dialog is now adjusted
dynamically based on the available space. This prevents some problems with
lower display resolutions.
3D viewer: loading of box volumes workes again.
The statistics widget back-end will now correctly use up-to-date time-zone
information for the query time range. This fixes some time zone conversion
corner cases.
Graph widget: SVG export works again. The exported SVG now groups labels with
node/edge. Now also single node exports are supported.
If Ctrl-Z was pressed and released very quickly, two undo steps were taken.
Now always only one undo step will be done per single Ctrl-Z click if not hold
down.
3D viewer: partner node spheres are now also shown for restricted connectors.
Multiple stack viewers no longer use the same ID to make requests to
the database.
The connector table can now be used as a skeleton source, where
previously an error would be raised.
The tag table now collapses any tags with identical names, but as a
consequence does not show the tag ID (as there may be multiple IDs)

POST /{project_id}/analytics/broken-section-nodes:
Get s list of all nodes that are currently located in a broken section of any
stack linked to their project. Obtionally, specific skeletons can be checked.

POST /{project_id}/skeleton/analytics
Is renamed to POST /{project_id}/analytics/skeletons.

None.

GET /{project_id}/stack/{stack_id}/models
Meshes have been replaced with volumes.