Python-catmaid

Contributors: Andrew Champion, Tom Kazimiers

Features and enhancements

3D viewer:

- The 'View settings' has a new option: 'Use native resolution'. When
activated (default), the native resolution of the current display will
be used. This improves image quality on HiDPI displays like Apple Retina.
If the performance penality is too big for large scenes, this can be
switched off again.


Connectivity Matrix:

- With the help of the "Export XLSX" button, the currently displayed matrix can
be exported as a Microsoft Excel compatible XLSX file. Colors are preserved.


Miscellaneous:

- With the help of the 'sg' and 'sgs' deep link parameters, stack groups can now
be loaded directly through a URL.


Bug fixes

- If multiple stack viewers are open, skeletons can now me modified again across
all open tracing layers. E.g. with orthogonal views, selecting a node in one
view and adding a child in another view work again.

Contributors: Andrew Champion, Tom Kazimiers

Features and enhancements

3D viewer:

- When coloring by creator the user colormap dialog only shows users who have
created at least one node loaded in the view. Additionally, a new coloring
mode, "By Creator (relevant users)", will generate a new set of colors for
these users from the CATMAID color scheme. This is useful if many users have
similar colors in their user profiles.

- Rendering and removal of skeletons is much faster, which is especially
noticeable for > 100 loaded skeletons. This also enables the use of a more
accurate node picking (Shift+click) algorithm as default, which before was
only used as fallback.


Volume manager:

- Volumes an now be removed (given a user has the required permissions) by
clicking on the 'remove' link in the last column of the volume table.


Statistics widget:

- If a user has the can_administer permission for a project, the Statistics
widget now displays an extra button to open the new User Analytics widget. It
displays the same information as the admin view with the same name. The user
analytics view now offers also options to adjust the max. inactivity time and
whether all write operations should be included (as opposed to only node and
review changes).


Tracing overlay:

- Radii can now be set to be visible for no nodes, the active node, all nodes
in the active skeleton, or all nodes through the Settings Widget.

- Pressing Ctrl + O will set a radius with the measurement tool without
bringing up the confirmation dialog.


Miscellaneous:

- Holding Ctrl with < or > will now smoothly animate through sections as
fast as the active layers will allow. This also works with Shift to move
10 sections at a time.

- The log now displays times in the local timezone.

- The connector table now lists the confidence of both the link to the
connector and from the connector to the target treenode.


Bug fixes

- Remove major cause of CATMAID freezing after the display of an error message.

- Annotation search lists all results again, not only first page.

- When joining skeletons, the creation time of annotations is preserved.

- Fixed an error preventing branching from virtual nodes in some cases.

- The history widget correctly displays the action time, not the current time.

Contributors: Andrew Champion, Tom Kazimiers

Notes

Contributors: Albert Cardona, Andrew Champion, Tom Kazimiers

Notes

- A virtualenv upgrade is required.
- PostgreSQL 9.5 and PostGIS 2.2 is now required. When updating, update PostGIS
first and update all databases in which the PostGIS extension is installed by
running "ALTER EXTENSION postgis UPDATE;". Then perform the Postgres update.


Features and enhancements

Tracing overlay:

- Visibility groups can be defined that hide or show nodes in the overlay
based upon filtering criteria such as neuron meta-annotations or node
creator. Unlike the skeleton source based visibility, visibility groups can be
toggled instantly with HOME (for group 1) or Shift + HOME (for group 2). For
meta-annotation based visibility, this does not require using a search as a
skeleton source, and the set of skeletons matched by the meta-annotations is
transparently refreshed in the background. Another visibility group,
"Always visible", establishes a set of filters for overriding hidden groups
such that skeletons matched by these filters will always be shown.

- The active node color for virtual nodes can now be configured to be different
than for read nodes.

- The active node color for suppressed virtual nodes can be configured to be
different than for unsuppressed virtual nodes. Note this only takes effect
if the "Respect suppressed virtual nodes during navigation" setting is
enabled.


3D viewer:

- Through the "List connectors" button on the Main tab, it is now possible to
open a connector selection with all currently loaded connectors in it.
Skeleton visibility and connector restrictions are respected.


Importer:

- Projects and stacks available on remote servers can now be imported,
optionally with API-key authentication on other CATMAID instances. The remote
data source can of course be any URL in a JSON or YAML format understood by
CATMAID. The import section in the CATMAID documentation holds more detail on
this. For CATMAID, the new "projects/export" endpoint provides all required
data that is visible to the requesting user.


Graph widget:

- The new button "Open Connectivity Matrix" in the Export tab will open a new
Connectivity Matrix widget for the current graph, including its groups.


Connectivity matrix:

- It is now possible to manually change the order of multiple entries at once,
which is useful to move sets of entries. The "Display" tab now has a "Manually
edit order" option. If checked, number input boxes are shown next to each row
and column head as well as a "Re-order" button in the top-left cell if the
table. After the numbers are adjusted to the desired order, the "Re-order"
button will apply the new ordering. Negative and decimal numbers can be used.

- Connectivity matrices can now be exported as PDF. The "Export PDF" button on
the "Main" tab will open a dialog explaining that this PDF export is made
through having the browser print the table and how to enable colors. Pressing
"Print" will show the browser's print dialog for only the table.


Settings widget:

- Tracing overlay colors customized in the settings widget are now persistent.

- Neuron name settings customized in the settings widget are now persistent.

- The delimiter used to separate annotations in a neuron name can now be
configured in the Annotations section of the Settings Widget.

- It is now possible to configure the available page length options used by
most tables from a central place. This is done through the "Table page length
options" setting, which is available from the Settings widget. For widgets to
be aware of page length setting changes, they have to be reloaded.


History tables:

- Starting with this release, CATMAID will record every single change to its
database tables in so called history tables. This makes it possible to
reconstruct the actual history of data (e.g. neurons) and user contributions.
Even data deleted in CATMAID can now be recovered without touching backups.

- The log widget in the front-end provides a way to few the history: It has a
new tab called "History", where each event that caused related database
changes is listed.


Miscellaneous:

- Alt + Y will always create a new selection table and add the active neuron
to it. Also works with Shift.

- Images on CATMAID's front-page are now loaded lazily, i.e. they are only
requested and shown once they come into view. This improves performance
significantly when displaying many sample images.

- New filter "Label Color Map" will false-color stacks of label ID images.

- The button "Add annotations to neurons" above annotation lists in the
Neuron Navigator makes it possible to send currently selected
annotations to other neurons. Those target neurons are selected by
choosing a skeleton source in a dialog box, which is shown to the user
once the button is pressed.

Bug fixes

- Additive blending between layers now works also when filters are in use. This
allows for proper in-browser composite generation.

- Hidden nodes are no longer selected by G or Shift + Y.

- All skeleton sources are now selectable when exporting NeuroML.

- Fix "Reset to inherited default" and "Lock this setting" buttons in settings
controls not being clickable.

- All layouts of the color picker can be used again (i.e. resizing it).

Contributors:: Albert Cardona, Andrew Champion, Tom Kazimiers

Notes

- The default image base setting for the importer has changed. If you use the
importer along with this setting, please update your settings.py file to now
use IMPORTER_DEFAULT_IMAGE_BASE instead of CATMAID_IMPORT_URL. The semantics
stay the same.


Features and enhancements

Graph widget:

- If a skeleton is appended that already exists in a group, the group's color
and label now doesn't change anymore. Instead a info message is shown.

- Selected edges can now be removed with the help of the "Remove" button in the
"Selection" tab. Also, a help text icon has been added to the title bar. The
widget help window currently only contains information on how edges/links
between nodes can be hidden.


Volume widget:

- Preview for alpha shapes is now disabled by default due to its potential
re-computation cost.

- Convex hull and alpha shape meshes are now only automatically re-generated on
property changes if preview is enabled.

- Saving a new volume makes sure the volume's mesh is up-to-date and will
re-generate it if needed. Re-generations will now also show an info dialog.
If no mesh could be generated, saving is not allowed and the edit form will
stay open.

- Two new filters for convex hulls and alpha shapes are now available: "only
end nodes" (optionally including the root) and "only branch nodes". These
will restrict the base point set for volume generation.

- Alpha shapes now use the inverse of the alpha value used so far. This makes it
easier to use since it translates directly into nanometers.

- If a synaptic connection filter is used with Alpha shapes and convex hulls, it
is now possible to select all synaptic nodes, regardless of the partner
skeleton (select "None" as partner neurons), and to select both pre- and
post-synaptic nodes at the same time.

- Alpha shapes now use a different implementation which takes a little bit more
time to compute, but doesn't require re-computation if different alpha values
are used. This makes finding a good alpha value much quicker. The input field
for the alpha value to use is now also a numeric field in which arrow keys and
mouse wheel can be used to change the value. A second numeric input allows to
change the step size of alpha value changes.

- For preview, volumes now use the color and opacity defined in the 3D viewer.


Tile layer:

- An efficient browsing mode is now available that will not load tiles at
the periphery of the stack viewer. This is useful to reduce data use and
browsing latency on bandwidth-limited connections. To use this mode, increase
the "Tile area efficiency threshold" in the tile layer controls.


3D viewer:

- Meshes and volumes can now optionally be displayed with visible faces instead
of wireframe only.

- Volume list is now updated when new volumes are added, re-opening the widget
is not required anymore.

- Transparent volumes are now displayed correctly.


Miscellaneous:

- If a client tries to perform an operation without having the most recent data
available and the performed action is canceled, a more helpful dialog is now
shown. It explains the situation and offers to refresh the client view
(currently only nodes in the tracing layer are refreshed).


Administration:

- The image data importer available from CATMAID's admin interface supports now
the specification of stack groups. It can also apply custom translations when
mapping imported stacks to imported projects.


Bug fixes

- Creating nodes using the Z key without other nodes in close proximity works
again.

- Zoom level slider initialized correctly for stacks with eight zoom levels.

- Showing connector info for edge in Graph widget (Alt+Click) now works also if
the source is a single neuron and the target a group or split node.

- Activate target node of a joined-in skeleton again.

Contributors: Albert Cardona, Andrew Champion, Tom Kazimiers


Features and enhancements

Miscellaneous:

- The skeleton projection layer can now draw the colors used from the selected
source. This is now the default and can be changed in the settings widget with
the help of the "Use source colors" checkbox.

- Unavailable images on CATMAID's front pages are now displayed as a gray
placeholder box, instead of the broken image icon of the browser.

- A new volume type was added: alpha shapes can now be created in practically the
same way as convex hull volumes are created. Alpha shapes have one additional
parameter: alpha. It is used to filter edges for result mesh and has to be
fairly low with our spatial dimensions. Values around 0.00001 seemed to work
well in some cases. The preview of alpha shapes is disabled by default, because
they can take much longer to compute.

- Materialized virtual nodes have now the correct edition time set, which make
operations like adding a child to a virtual node work again (state checks
prevent this with wrong edition time).

- The neuron search will now show a warning and cancel a search if a query
annotation doesn't exist and the query term doesn't start with a forward
slash (used for regular expressions).


Bug fixes

- Creating synaptic connections from connector nodes across sections works
again.

- Inserting a node along an edge will now render correctly right after using
ctrl+alt+click.

- Merging two skeletons while the losing skeleton was loaded into another widget
(e.g. Selection Table) doesn't trigger an error anymore.

- Undoing confidence changes works again.