2017.05.17

2017.05.17

Contributors: Andrew Champion, Tom Kazimiers

Notes

• A virtualenv upgrade is required. To correctly install one updated dependency, the django-rest-swagger Python package has to be removed first from from the virtualenv, before the virtualenv is updated:

  pip uninstall django-rest-swagger
  pip install -r requirements.txt

Features and enhancements

Widget state saving:

• Infrastructure has been added to store widget configuration client side in a browser cookie. This makes it easy to update widgets to support automatic saving and loading of state information. The automatic saving and loading behavior can be configured in the General Settings section of the Settings Widget. To explicitly save the state in a supported widget, the respective button available through the "Window Configuration" title bar icon can be used as well.

• State saving support has been added for the 3D Viewer and the Connectivity Widget.

Generic node filtering:

• A generic user interface for filtering nodes is now available to widgets. If a widget supports it, the filtering user interface is available through the filter icon in the widget's title bar.

• The user interface has a "Filters" tab which lists all active filters for a widget and a "Add filter" tab, which can be used to create new filter rules.

• Filter rules select nodes that are kept, i.e. the filter application results in a list of nodes that match the filter expression.

• Different filter types are available at the moment: Only end nodes, only tagged nodes, only nuclei, only a sub-arbor starting from a tag, tag defined region, created by user(s), node creation/edite time, binary split, axon, dendrite, synaptic connectivity and volumes. Some come with own user input elements, but all can optionally be applied to only a subset of skeletons.

• Multiple filters can be combined, e.g. all branch nodes with a particular tag and end nodes. All filter rules are combined in a left-associative fashion and union and intersection can be used as operators.

Connectivity widget:

• Support for node filtering has been added, it can be configured through the filter icon in the title bar. All features listed under Generic Node Filters are supported. If a node of a skeleton from the top list doesn't match the filter expression, synaptic connections involving it will not be respected.

Review widget:

• Whether detailed review colors should be used is now persisted.

• The checkbox "Save review updates" allows to disable sending review updates to the server. Ending review or closing the widget will cause all review updates to be lost. If disabled, a warning is displayed. This is useful to only use the "navigational" features of the review widget.

• Support for node filtering has been added, it can be configured through the filter icon in the title bar. All features listed under Generic Node Filters are supported. If nodes are filtered, all percentages are relative to the filtered set of nodes.

3D viewer:

• The color of custom tag spheres can now be adjusted through a "color" button right next to the custom tag pattern.

• The color of the floor can now be adjusted though a "color" button next after the "Floor" checkbox.

• Skeleton coloring can now be set to not interpolate between different vertex colors and instead use always child colors for an edge.

• The color and whether to display mesh faces of individual volumes can now be adjusted more easily. A color selector is available right next to the checkbox of each visible volume in the volume drop-down menu. The global color controls are used as default for newly displayed volumes.

• Support for node filtering has been added, which can be configured through the filter icon in the title bar. All features listed under Generic Node Filters are supported.

Tracing layer:

• When inserting a new node between two existing nodes, the new node's user will now be the logged in user as long as the skeleton is not locked. This makes it easier for reviewers to make corrections, because the new node can now be moved (instead of only initially placed). If the neuron is locked, it is only possible to create a collinear node between parent and child with the child's user (e.g. through tagging a virtual node).

Miscellaneous:

• When a node is selected a minimal node status line is now shown again using information already available in the client. If the "Show extended status bar information" setting is the Settings Widget is checked, additional information is fetched from the back-end.

• The SWC export by default now maps real node IDs to incremental IDs starting with 1 from the root node, which is something some SWC tools expect. To disable this uncheck "Linearize IDs" in the SWC export dialog.

• Neuron Navigator: It is now possible to delete multiple neurons from a neuron listing.

• The importer widget now allows to allow multiple SWC files at the same time.

Bug fixes

• Export widget: The SWC export link works again.

• Tracing tool: using the personal tag set doesn't remove existing tags anymore when added or removed.

• Fix catmaid_insert_example_projects management command.

• Review widget: it is possible again to use Q/W to move along already reviewed segments (re-review of nodes).

• Fix some accidental key mapping collisions of some special keys and media keys.

• Connector nodes can be deleted again right after they were created.

• 3D viewer: connector links are displayed again if connector restrictions are in use.

• Radius creation works now in orthogonal views as expected.

API Changes

Additions

• None.

Modifications

• POST /{project_id}/skeletons/connectivity:
  If the new "with_nodes" parameter is true, the involved treenode links are
  also returned for each partner.

Deprecations

• None.

Removals

• None.

2017.04.20

2017.04.20

Contributors: Albert Cardona, Tom Kazimiers

Notes

• A virtualenv update is required.

• The location of the manage.py script changed: it moved a level up into django/projects. All other configuration files remain where they are. Make sure to update your settings.py file by replacing the line from settings_base import * with from mysite.settings_base import *.

• Python 3.5 is now experimentally supported. Most functionality should work without problems. To test, make sure to update settings.py by replacing the fragment hashlib.md5(CATMAID_URL) with 'hashlib.md5(CATMAID_URL.encode('utf-8'))'.

• To use the skeleton import API users or groups now need to have the can_import permission.

Features and enhancements

3D viewer:

• Nodes on specific section of the focused stack can now be automatically moved to an interpolated location. The "Skeleton filters" tab provides now options to either interpolate nodes on broken sections or a custom list of sections. The new location in the average X/Y location of the parent and child. If only parent or child is available (leaf or parent), its X/Y location is used.

• An started animation export can now be canceled through a "Cancel" button.

Review widget:

• Segments can now be reviewed in downstream order by unchecking the "Upstream review" checkbox. Q will still move downstream and W upstream. Already reviewed nodes are skipped in both directions.

• Only show "Done" message if 100% are reviewed in one of the selected columns, including Team. Team is now checked by default.

Import Export widget:

• The Export Widget has been renamed to "Import Export Widget", along with it its short-name for Ctrl+Space.

• If a user has import permissions on a project, an "Import" and an "Export" tab are displayed. The new import tab contains a simple SWC import, which allows to select an SWC file and import it. If successful, the new skeleton is selected right away.

Neuron Navigator:

• Instead of a "Last used" column annotation tables now show an "Annotated on" column. The last used date used before reflected the last change of an annotation itself. Now the creation time of the link relation is displayed, which doesn't change during a merge or split operation, unlike "edition time".

Splitting and merging:

• In the split and merge dialog, instead of selecting the skeleton/part with more nodes as default "winning" skeleton, the skeleton with a greater cable length is now chosen as default "winning" skeleton.

• Keep original creation time and edition time of annotation links that are copied to the newly created part on a split skeleton.

• When skeletons are merged and share annotations that should be kept, the older annotation link creation time will now be stored in the final neuron annotation link.

Miscellaneous:

• Refreshing the nodes on the StackViewer will not print the info on the active node in the status bar. This saves one additional request to the server, speeding up tracing from high-latency locations such as overseas.

• The Measurement Table now highlights the active skeleton.

• Alt+T can now be used to tag a node with a predefined set of tags. This set can be configured through the Settings Widget, using the "Personal tag set" field in the Tracing section.

• The SWC export button in the Tracing Tool toolbar has been replaced with an Export Widget entry. Additionally, SWC files for multiple skeletons can be created at the same time and exported together in a Zip archive.

• Many widgets can now have aliases, which will be displayed in parentheses after the name in the window title bar. A small window-like icon next to the window name toggles controls to change the widget alias.

• Review status colors can now be more fine-grained. The Settings Widget contains now the option "Use detail review color status" as part of the Tracing section. If enabled, ten different colors plus the regular 0% and 100% color will be used instead of three.

• Generating the URL to a view now respects loaded stack groups. If a stack group was initially loaded, it is included in the URL.

• It is now possible to control the number of sections moved when Shift is pressed while using ",", "." or the mouse wheel. This step size is controlled through the "Major section step" setting in the "Stack view" section of the settings widget. Alternatively, for a dialog to set a new step size, the key combination Shift + # can be used.

• The Connector Table now also displays the link creation time besides the edition time.

• Tracing layer: Moving to a child node using "]" doesn't query the server anymore if child info is already available in client.

Bug fixes

• 3D Viewer: active node sphere is now hidden if no node is selected.

• Image data layers that are added to a stack viewer will be added after the last existing image data layer and before other layers. This makes sure tracing data stays on top.

• Selecting an unreachable mirror won't hide the tracing layer anymore.

API Changes

Additions

None.

Modifications

• GET /messages/mark_read: This API took a message ID as parameter before and is replaced by: POST /messages/{message_id}/mark_read

• POST /{project_id}/node/user-info: The node_id parameter has been replaced with a node_ids parameter, which is expected to be a list of node IDs. The response maps now individual info objects to their respective node IDs.

• GET /{project_id}/connectors/ Each result link now contains one additional column: the link's creation time. It replaces the edition_time in column nine. The edition time is now available in column ten.

Deprecations

None.

Removals

None.

2017.03.16

Contributors: Albert Cardona, Chris Barnes, Tom Kazimiers, Andrew Champion

Notes

• A virtualenv update required!

• The 'classic' node provider has been removed, use 'postgis3d' or 'postgis2d'
  instead.

• Performance of the default node query strategy (NODE_PROVIDER = 'postgis3d')
  improves now when connection pooling is used and PREPARED_STATEMENTS = True.

• Both 'postgis2d' and 'postgis3d' node providers support now prepared
  statements for connector queries.

• PyPy is now supported and can be used to improve performance of back-end heavy
  endpoints. Most functionality is available, except for the following: Ontology
  clustering, Cropping, Synapse clustering, HDF 5 tiles and User analytics. To
  use PyPy, a new virtualenv using the PyPy executable has to be created.

• There is now a catmaid_prewarm_db management command, which can be used to
  populate OS and database buffers with heavily used tables.

Features and enhancements

Graph widget:

• The "Selection" tab now has two new buttons that provide the ability to invert
  the selection, and also to select graph nodes based on matching a text string
  or by a regular expression (when the text starts with a '/').

3D Viewer:

• With the help of the new "Update active" checkbox in the "View" tab it is now
  possible to automatically update the active skeleton if it changes.

• It is now possible to hide edges that represent a link between a node and a
  connector. This is also respected with connector restrictions enabled and can
  be set with new "Show connector links" checkbox in the "View settings" tab.

Selection table:

• To prevent accidental sorting the new "Lock order" checkbox can be enabled.
  Clicks on the table headers will have no effect if the order is locked.

• Two new action icons are added on the right of each row: move a skeleton up or
  down in the table.

Annotation graph:

• A new 'Annotation Graph' widget provides a graph like visualization of
  CATMAID's annotation space, which is mainly useful to visualize annotation
  hierarchies. Meta-annotation are linked to annotations through edges. This
  widget can be opened with Ctrl+Space together with the 'annotation-graph'
  keyword.

• Optionally, the minimum and maximum number of linked annotations in a single
  hierarchy can be configured.

• Selecting an annotation will query all (sub-)annotated skeletons, which can be
  used as through a regular skeleton source selection in other widgets.

Miscellaneous:

• Tracing tool: the "Show labels" setting is now remembered across sessions.

• Right clicking on a stack viewer won't bring up the browser context menu
  anymore. Instead, the right mouse button can now be used for panning, too.

• The merge dialog has now a "Swap" button in the lower left corner. It can be
  used to swap winning and losing skeleton in a merge.

• Add a 'select' tracing modes to the tracing tool: Clicking an active skeleton or
  synapse tracing mode button (first two buttons in toolbar) will switch to the
  select mode where clicking doesn't create new nodes.

• The layer settings of image data layers allow now to add custom mirrors,
  which is useful to e.g. make a local copy of the image data availabl in
  CATMAID. This can reduce latency due to remote image loading considerably. See
  the user FAQ in the documentation for more details.

• Annotation pages in the Neuron Navigator now also list meta annotations and
  provide a way to de-annotate them.

Bug fixes

• Fix occasional tracing overlay resizing problem where a portion of the screen
  would not show tracing data, but also won't update.

• 3D viewer: broken sections can now be displayed again.

• 3D viewer: the Z plane with stack images will now render correctly for the
  default maximum zoom level.

API changes

Additions

None.

Modifications

None.

Deprecations

None.

Removals

None.

2017.02.16

2017.02.16

Contributors: Chris Barnes, Albert Cardona, Andrew Champion, Tom Kazimiers

Notes

• A new TREENODE_PROVIDER option can be added to settings.py, which can be used
  to configure the way node queries are executed. Options are 'classic',
  'postgis3d' and 'postgis2d'. Depending on your environment, 'postgis2d' might
  be fastest, but 'postgis3d' is the current default (i.e. what has been used so
  far).
• The new PREPARED_STATEMENTS option can be added to settings.py and set to
  True to improve node query performance when connection pooling is used.
  Without connection pooling, this setting hurts performance, which is why it is
  set to False by default.
• Stack mirrors (see below) are not displayed by default in CATMAID's standard
  data views. To show them, '"show_mirrors": true' (including double quotes) has
  to be added to the respective data view configuration in CATMAID's admin
  interface.

Features and enhancements

Stack mirrors:

• To reduce loading time of image data from different places around the world,
  it is common to copy the image data set and make it available from a server
  closer to its users. These "stack mirrors" are now handled differently by
  CATMAID. Until now it was common to select the closest mirror manually by
  clicking on an image on CATMAID's project list or by clicking on the
  respective link. To select a particular "stack mirror" one now only links can
  be used, individual images are not shown anymore. If no images were used
  before and only links were shown on CATMAID's home page, only small visual
  change was mode: an extra stack link on top of all mirrors is added. As an
  alternative to selecting individual mirrors, both, images and stack links can
  now be used to open a stack as well and CATMAID selects the fastest mirror
  automatically.
• When using links to a particular view in CATMAID ("URL to this view"), CATMAID
  will automatically select the fastest available stack mirror.
• Once a stack is displayed the stack mirror in use can be changed: After
  clicking on the white-on-blue square in the lower left corner of the image
  data display, the image display settings will show up. In there the active
  mirror can be selected from a drop-down list.

Treenode Viewer:

• A new tool similar to the connector viewer, which allows users to
  quickly view the nodes in a treenode table.
• The viewer is opened from the treenode table.
• Nodes are shown only if they are filtered in the table, and appear in
  the order that they appear in the table.
• When the sorting and filtering in the table is changed, users can
  refresh the viewer from the table to reflect these changes.

Connector Viewer enhancements:

• Connectors can now be constrained by their pre-synaptic and post-synaptic
  skeletons.
• If either is unpopulated, it is unconstrained on that side (i.e. all
  outgoing connectors can be found by clearing the 'Post- skeletons' set).
• Sorting algorithms based on treenodes associated with the connector
  (e.g. depth) can be applied either to presynaptic or postsynaptic
  skeletons.
• The 'Reverse' button switches the contents of the two skeleton sets.
• The 'Sync' checkbox sets the pre- and post- synaptic sets to have the
  same contents (the union of their contents when the box is checked)
  and keeps them that way: this is useful for inspecting all connectors
  acting within a set of skeletons, such as reciprocal connections.
• For undirected connectors (gap junctions, abutting etc.), you can use
  either the 'pre' or the 'post' set. If both sets are populated, only
  connectors touching a pre- skeleton and a post- skeleton (with 2
  distinct edges) will be shown.
• When using the connector viewer as a skeleton source, the output is the
  union of the two skeleton sets.
• The controls have been separated out into tabs.
• N.B.: Because the Connector Viewer is now populated in a different way
  to the Connector Table, you can now only open a Table from a Viewer if
  one of the skeleton sets is empty, and a connector type other than 'All'
  is selected.

Miscellaneous:

• Bookmarks are now persistent for each project.
• The Graph Widget now offers two options when exporting SVGs: regular ones and
  Adobe Illustrator compatible ones (because Adobe isn't SVG standard conform).
  An option dialog is shown after clicking "Export SVG".
• From the Graph Widget exported SVG files preserve now the view of the widget
  (zoom and pan).
• The tag table can now be constrained by a set of skeletons.
• The tag table now gives the user information on how many skeletons are
  being used as constraints, and how many tags/skeletons/nodes are
  selected.
• When the tag table is refreshed, the filters and the last sort are
  persisted.
• The treenode table can now be filtered by node confidence, creator and
  reviewer.
• When creating new volumes with the help of the Volume Manager, the color and
  opacity of the 3D preview can now be adjusted.

Bug fixes

• 3D Viewer: custom tag highlighting now also works for tags with upper case
  letters.
• Layer settings: checkboxes now have correct default value.
• Tag table: any tags with identical names are now treated as identical.
• Tag table: fixed off-by-one error in node count.

API Changes

Additions

None.

Modifications

• POST /{project_id}/node/list and POST /{project_id}/node/list:
  The returned timestamps are now second based UTC epoch numbers instead of UTC
  strings.

Deprecations

None.

Removals

None.

2017.01.19

2017.01.19

Contributors: Chris Barnes, Andrew Champion, Tom Kazimiers

Notes:

• 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.

Features and enhancements

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.

Bug fixes

• 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)

API Changes

Additions

• 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.

Modifications

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

Deprecations

None.

Removals

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

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.

2016.11.04

2016.11.04

Contributors: Gregory Jefferis, Tom Kazimiers

Notes

• Virtualenv update required

Features and enhancements

Tracing layer:

• Alt+Click so far created gap junction connectors. This behavior is replaced with opening a small context menu that provides access to all currently available connector types (abutting, gap junction, presynaptic, postsynaptic). Optionally, through the Settings Widget, remembering the last connector type created can be enabled. If this is the case, regular Shift+Click behavior is to create the last connector type, as opposed to pre/post-synaptic connectors.

3D viewer:

• History replay now has a reset button to load the most recent version of each skeleton. The new pause button will stop the animation at the current time and pressing start will resume playback. Additionally, a slider control now allows to move to arbitrary points in time of the history animations. Touching the slider will automatically pause the replay.
• History replays can now be exported.

Neuron dendrogram:

• Controls are now organized in tabs and a new setting was added to change the line width.

Miscellaneous:

• If users have sufficient permissions, they can click on individual names in the Project Statistics Widget to show a User Analytics window for the respective user and currently selected time frame.
• Pressing Ctrl+Space will now open a dialog which allows opening a widget based on its short name (e.g. neuron-dendrogram) or parts of it.
• A small system check widget has been added, mainly useful for development. It currently only supports FPS measurement and can be opened by pressing Ctrl+Space and entering "system-check".

API Changes

Additions

• GET /{project_id}/skeletons/{skeleton_id}/compact-detail
  Provides same functionality as
  GET/POST /{project_id}/{skeleton_id}/[0|1]/[0|1]/compact-skeleton, but uses
  explicit GET parameters.
• POST /{project_id}/nodes/
  Provides the same data as the former POST /{project_id}/nodes/list and takes
  the same parameters.

Modifications

None.

Deprecations

• GET/POST /{project_id}/{skeleton_id}/[0|1]/[0|1]/compact-skeleton
  This endpoint will be replaced in the future with the newly introduced
  endpoint GET /{project_id}/skeletons/{skeleton_id}/compact-detail.
• POST /{project_id}/node/list
  This endpoint will be replaced in the future with the newly introduced
  endpoint POST /{project_id}/nodes/. It takes the same parameters.

Removals

None.

2016.10.18

2016.10.18

Contributors: Andrew Champion, Tom Kazimiers

Features and enhancements

3D viewer:

• Picking now respects the Z plane. if displayed. Shift+click any location on
  it and the stack viewer position is changed accordingly. This works just like
  picking nodes, except that the active node doesn't change.
• The original camera location is now restored by default after exporting an
  animation.
• A new tab called 'History' gives access to tools for replaying the
  reconstruction of the currently loaded skeletons. The time range as well as
  the time advance per frame can be adjusted. By default, the time range covered
  starts ith the first change and ends with the last one (when no custom date is
  entered). Optionally, empty bouts where no changes happend will be skipped if
  a length (in minutes) is specified. If not disabled through the 'Include
  merges' checkbox, arbors that only where merged in at one point will also be
  displayed before such a merge. Tags on individual nodes are currently hidden
  during animation.

Review widget:

• Skeleton Analytics, which was a separate widget before, is now available
  through a new tab in the Review Widget. It still lists the same problems for
  selected neurons as before (i.e. missing end tags).

Connector table (available through Neuron Navigator):

• Support for abutting connectors and gap junctions has been added.
• The displayed table can now be exported as CSV file.
• The listed information for connector relations with only one partner is now
  consistent with multi-relation cases: the linked node ID, node location and
  skeleton ID are shown instead of the connector location along an empty node
  and skeleton fields.
• The widget can now pull skeletons to list connectors for from other skeleton
  sources. It acts itself as a skeleton source as well and provides all result
  skeleton IDs.

Importer:

• The project and stack importer now supports the customization of when projects
  are considered known as well as what to do with known projects: ignore, merge
  or replace.
• If remote hosts are used as a project or stack import source, HTTP
  Authentication can now be used to get access to a server.

Miscellaneous:

• The tracing tool has a new icon.
• If users get a permission denied error (e.g. due to being logged out or just
  having not enough permissions), a login dialog is now shown. It allows users
  to re-login or change the user entirely. The action causing the permission
  error, is not repeated automatically.
• Using brackets to navigate along a skeleton now also works if the
  reconstruction data is hidden (e.g. when the space bar is held down).

Bug fixes

• The statistics widget now properly respects time zones when grouping by day.
• Partner neurons listed in the Connectivity Widget can now be filtered again
  with regular expressions (when the filter pattern starts with "/").
• Loading stack groups through URLs now correctly respects the specified location.
• H works correctly when a virtual node is active.
• Pressing E in the Review widget now works again when a segment was completely
  reviewed.
• The group membership permission tool in CATMAID's admin area works with groups
  again.

API Changes

Additions

• GET /{project_id}/connectors/
  Replaces the POST /{project_id}/connector/table/list endpoint, but also
  changes the parameter names. Additionally, the "relation_type" parameter is
  now expected to contain the actual relation name instead of a numeric alias:
  The value "0" is replaced with "postsynaptic_to" and "1" is replaced with
  "presynaptic_to". See /apis documentation for details.

Modifications

• GET/POST /{project_id}/[0|1]/[0|1]/compact-skeleton
  The new parameter with_history allows to include historic data in th
  response. Will also include timestamps for regular nodes.

Deprecations

None.

Removals

• POST /{project_id}/connector/table/list
  This endpoint is replaced by the GET /{project_id}/connectors endpoint,
  described above.

2016.09.01

2016.09.01

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.

API changes

None.

2016.08.26

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.

API changes

Additions:

• None.

Modifications:

• None.

Deprecations:

• None.

Removals:

• GET /{project_id}/stats
  This endpoint returned an HTML document displayed by CATMAIDs statistics
  widget.