Release 2015.3.31

Contributors: Albert Cardona, Andrew Champion, Tom Kazimiers, Stephan Gerhard

Features and enhancements

Key shortcuts / mouse operations:

• Shift+T removes all tags from the currently active node.
• After using R to go the nearest open leaf, shift+R cycles through other open
  leaves in the skeleton in order of ascending distance from the starting
  location. Combining alt with these operations orders open leaves by most
  recent creation instead of distance.
• Ctrl+Y removes the active skeleton from the last used selection widget.
• Shift+Y selects skeletons within a radius of the active node in the tracing
  layer and adds them to the last used selection widget. Ctrl+shift+Y works in
  the same way to remove skeletons from the last used selection widget.
• If the next (or previous) branch/end point is already selected when V (or B)
  is pressed, the view will center on it nevertheless.
• If the mouse is over the stack when zooming, the view will recenter so that
  the same stack location remains under the mouse at the new scale.
• During review, Q and W during will refocus on the last reviewed neuron if
  review is interrupted (another node is selected), regardless of the auto
  centering setting. If one looks beyond the current segment, the last reviewed
  node will be selected by Q and W as well, but auto centering is respected.

Review system:

• New "Reviewer Team" system allows filtering reviews in visualizations and
  statistics to include only those by particular reviewers. Each user can
  control which reviewers to include in her team. A date can be configured for
  each reviewer in the team, so that only reviews from that reviewer after this
  date are included.
  • A user's reviewer team is configured through the Settings widget.
  • The review widget includes a team column between the user and union columns.
  • The percent reviewed column in the selection widget can be set to team or
    union.
  • Team review coloring is available in the 3D viewer and group graph.

3D viewer:

• With Ctrl + mouse wheel, only the camera is moved in target direction, the
  target stays fixed. If Alt + mouse wheel is used, the target moves as well.
• The CSV export not also includes the parent ID for each node, which can be
  used to reconstruct the topological tree.
• The auto-created selection widget is now 50% smaller, giving more vertical
  space to the 3D viewer.
• With the help of controls of the Animation tab, simple animations can be
  played. Currently, rotation around the X, Y and Z axis as well as the current
  "up" direction of the camera. is supported. The back-and-forth mode will
  reverse rotation direction once a full circle is reached. With the help of the
  stepwise visibility option, individual neurons can be made visible after a
  certain amount of time the animation is running. Additionally, neurons can be
  made sequentially visible after each rotation.
• Animations can also be exported as WebM movie file. The "Export animation"
  button in the Export tab, will show a dialog with basic export settings. Like
  with the other view export options, the current 3D view setup is used. The
  frame size can be adjusted in the export dialog. Creating the file can take
  some seconds and currently only works for the Chrome browser (due to the lack
  of WebP support in others). The resulting WebM video file can be converted to
  any other format using e.g. VLC player, if needed.
• New shading mode "synapse-free chunks". Has one parameter, the minimum amount
  of synapse-free cable to consider between two consecutive synapses, adjustable
  from the "Shading Parameters" tab.
• New shading mode "dendritic backbone". Depends on 'microtubules end' tags, or
  will approximate twigs by using the Strahler number entered in the "Shading
  Parameters" tab.
• The view settings tab now contains a control to scale the size of the node
  handles (e.g. active node, special tags).

Tile layer:

• Tiles can now be rendered with WebGL, which enables new visualization features
  and fixes some flickering issues. Enable via "Prefer WebGL Layers" in
  Settings. The WebGL renderer is currently considered experimental and may have
  stability issues on some clients. See
  #186 (comment) for
  details on using WebGL layers with your image stack host.
• The blend mode used to combine stacks and overlays is now configurable when
  using WebGL. This greatly improves visualization of confocal and other
  multichannel data. Blend mode is selectable from the layers control, activated
  via the toggle at the bottom left of the stack view.
• Filters can be applied to layers when using WebGL. Filters can be added and
  removed from layers through the layers control. Available filters currently
  include:
  • Gaussian blur
  • Color inversion
  • Brightness, contrast and saturation adjustment
  • Color matrix transform

Connectivity widget:

• It is now possible to remove added neurons again. Each row of the table of
  target neurons now contains a small 'x' icon in the first column to remove it.
• The selection column is not included anymore in the CSV export.

Analyze Arbor:

• Options are provided to approximate twigs by using a branch Strahler number
  defined in the "Options".
• Dimensions of the pie charts and XY plots is now configurable from the
  "Options" dialog.

Graph widget:

• New button to "Clone" the graph widget: opens a new widget with identical content.
• New buttons to "Save" and "Open..." to/from JSON, so that complex graphs can be
  reloaded later on. Skeletons not present in the database are not loaded.

Miscellaneous:

• Selecting tags for highlighting in the neuron dendrogram
• Synchronization between widgets was improved. Deleting a neuron in one widget,
  will remove it from other widgets as well.
• Hovering over the CATMAID text on the front page will display CATMAID's
  version.

Admin:

• For projects, stacks, overlays and data views there is now the option to
  duplicate objects from within the admin view. To copy objects without their
  relations, there is now a new action in the list view's action menu. To
  duplicate an entity with its relations, select the object and use the "save as
  new" button.

Export:

• A basic JSON export of all treenodes and connectors of the selected neurons is
  now possible.

Bug fixes

Tracing overlay:

• Trying to remove a non-existent tag from a node now doesn't show an error
  dialog anymore, but only a notification.

Key shortcuts / mouse operations:

• Fix bug where tagged nodes were not considered open by R regardless of tag
  content.

Neuron search:

• Make neuron names wrap and use the next line, if there is not enough space for
  it. This makes the table not expand in width until the name fits anymore.

3D viewer:

• Picking a synapse or other selectable elements is now more robust and now
  works also in orthographic mode.
• The projection mode (orthographic or perspective) is now also stored in a
  saved view.
• The 3D viewer's drawing canvas is now correctly sized again. Since the tab
  panel has been introduced, the 3D viewer has been too high. Now the
  pre-defined views (XY, XZ, ZY, ZX) are display correctly again, i.e. the whole
  bounding box is now seen again.
• Performance enhancement when smoothing skeletons with a Gaussian by avoiding
  to update the same Vector3 instances twice.

Reviews:

• Pressing 'E' during review will now go to the next unreviewed segment as seen
  from the currently reviewed one. Before, the first unreviewed segment as seen
  from the top of the table was selected.
• Pressing 'Q' on the first node (leaf) brings one back one section to check if
  the segment really ends. Pressing 'W' afterwards now brings one back to the
  first node, not the second like it has been before.

Connectivity widget:

• CSV export works again.

Miscellaneous:

• Vertical resizing of widgets now doesn't lead to strange size changes anymore.
• An alternative DVID tile source was added to support its multiscale API.