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Release 2015.1.15
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@tomka tomka released this 22 Jan 19:30
· 9918 commits to master since this release
r2015.1.15
1241e62

Key shortcuts / mouse operations:

  • A new shortcut key to navigate to a node's child has been added: ]. It
    behaves like V by navigating to the largest descendant branch. With
    Shift+] one cycles through sibling branches in order of descending
    size.
  • For consistency, the P shortcut to navigate to the parent has been
    replaced with [.
  • Navigation to the next branch has changed a bit: The V key now moves
    to the next branch node or end of the largest descendant branch of the
    active node, and subsequent presses of shift+V cycle through other
    possible descending branches in order of decreasing size.
  • While editing the radius of a node with the help of the surrounding
    circle, a click will confirm the current radius (not only pressing 'o'
    again). The radius editing can now also be canceled with the Esc key.
  • With Ctrl+Alt+click one can now insert a node into the active
    skeleton between two existing nodes.

Zoom:

  • Zooming is now also possible in smaller steps. The plus and minus
    buttons zoom in steps of 1 and with having the Shift key pressed
    additionally, steps of 0.1 are used.

3D viewer:

  • New export options (Export tab):
    • CVS representation of the rendered skeletons;
    • PNG and SVG image of the current view;
    • SVG catalogue of the current view. The catalogue contains each
      neuron a separate panel on the same SVG document--very useful to
      generate figures for a paper. Options are provided to sort and arrange
      panels, and to define pinned neurons that appear in each panel (e.g. a
      somatosensory axon that acts as reference for each neuron connected to
      it).
  • New "Spatial select" button (Main tab) that allows to select
    skeletons near the active node or connected to the active skeleton,
    within a specified distance. Matching skeletons will be shown in a new
    selection table. This is useful to e.g. select all single-node
    skeletons connected to the dorsal lobe part of a Kenyon cell.
  • Supports orthographic projection (see checkbox in View tab) so that
    no perspective distortion is applied and distances become comparable
    between different parts of the view.
  • The 3D viewer now has the option to follow the active node (View
    tab). This acts like clicking "Center active" after each active node
    change.
  • One can bookmark views in the 3D viewer, by pressing "Save view" in
    the Main tab. Views can be loaded by selecting them from the drop down
    list next to the button. These bookmarks are currently discarded once
    CATMAID is reloaded.
  • When Ctrl is pressed while zooming in the 3D viewer with the scroll
    wheel, the camera is actually moved towards its target. This is useful
    to overcome zooming limits and strong perspective distortion due to a
    high focal length when zooming.

Selection table:

  • "Randomize colors" in the selection table was replaced by a drop
    down list with different color schemes and the button "Colorize" to
    apply the selected one. The default is the coloring scheme that
    existed before. Some of the new color schemes are from Cynthia Brewer
    (see http://colorbrewer2.org/ ).
  • Neurons are activated by clicking on the name, like in all other
    widgets. The green tick icon has been removed.
  • New check box for each neuron called "meta" to toggle the display of
    extra information like the orange spheres for specially tagged nodes
    (TODO, uncertain end, etc.) or low confidence nodes.

Dendrogram:

  • Can now collapse nodes belonging to a branch that ends in a node
    tagged "not a branch".
  • One can now highlight multiple tags in the dendrogram by separating
    them with commas.

Graph widget:

  • Subgraphs (like axon & dendrite) can now be reset in the graph widget.

Annotations:

  • When adding an annotation, the pattern "{nX}" can be used to add an
    automatically incrementing number to each neuron annotated, starting
    at X. So if e.g. three neurons are annotated at once with the
    annotation "test-{n5}", the first one is annotated with "test-5", the
    second one with "test-6" and the last one with "test-7". Omitting X
    will be interpreted to start from 1.
  • When skeletons are joined, the name of the "losing" skeleton can now
    be added as an annotation to the "winning" skeleton right in the
    dialog. Its checkbox is unchecked by default, if the name follows the
    auto-generated name pattern "neuron 12345".

Searching:

  • The neuron name input boxes in both search widgets will now remember
    entries that have been used before.

Handling the unexpected:

  • A general error handler has been added so that CATMAID should
    hopefully not crash anymore, even if an error occurs. In such
    situations an error dialog is shown and the error is logged on the
    server so that we can investigate better what went wrong.

General neuron tracing:

  • A robust synapse clustering method was added: centrifugal synapse flow
    centrality. Many widgets now support a new method for finding axons based on it
    (e.g. in the 3D viewer as a shading method.
  • The connector table now displays the confidence of each link
  • Basic import/export support was added. There are two new management commands
    that can be used by admins to import and export tracing data.

Users and groups:

  • Support user registration (disabled by default). Default user groups for new
    users can be set.

Miscellaneous:

  • A new ROI tool was added, which can be activated for each user through the
    user settings. It currently supports only the creation of new ROIs. Additional
    sub-tools will be added for more functionality.

Contributors:

This update brought to you by Tom Kazimiers, Andrew Champion, Stephan
Gerhard and Albert Cardona.

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