2015.7.6

2015.7.6

CATMAID now uses the GPLv3 license and moved away from the stricter
AGPLv3. This move was discussed with all previous contributors and
agreed on. See the corresponding commit for more details.

Contributors: Albert Cardona, Andrew Champion, Tom Kazimiers

Notes

This release includes database changes that require manual intervention if you
are upgrading from an existing installation. A new dependency is now required:
PostGIS, an extension to PostgreSQL. After its installation, it has to be
activated for the CATMAID database. To do so, connect to the database using a
Postgres system user. Assuming a Postgres system user named "postgres" and a
CATMAID database named "catmaid", this could be done by calling

sudo -u postgres psql -d catmaid

Being connected to the database, PostGIS can be enabled by executing

CREATE EXTENSION postgis;

Now PostGIS is enabled and the connection can be closed again. Now a regular
update can be performed. Please note that this update can take quite some time
to complete. On bigger neuron tracing installations, multiple hours are
realistic.

Features and enhancements

Key shortcuts / mouse operations:

• Ctrl + mouse wheel now zooms the stack, while shift zooms by smaller
  increments.
• Pressing X in the tracing tool will begin measuring distance from the current
  cursor position. The mouse wheel can be used to measure along the stack Z
  axis. Clicking will close the measurement tool and show the final distance in
  the status bar. ESC cancels the tool.

Multi-view tracing and virtual nodes:

• Orthogonal views on a regular XY stack can now also be used for neuron
  reconstruction. If they are available as CATMAID stacks and opened while the
  tracing tool is activated, tracing data will be shown in the respective
  orthogonal views as well. Tracing can be done in these views just like in the
  regular XY view.
• When tracing, it is not required anymore to place a node in every section. If
  no node has been placed in a section, CATMAID will place a so called virtual node
  where the skeleton and the section meet. If this virtual node is modified in
  any way, e.g. tagging, joining, moving, etc. it will be created. This also
  slightly changes the way reviews work. Review information is only stored on
  real nodes.
• The review widget has a new settings: in-between node step. It specifies how
  many sections can be skipped between adjacent real nodes. This is done with
  respect to the currently focused stack. This stack is also used to determine
  in which direction to move to look beyond the start of a segment.

Stack viewer:

• Other stacks in a project can be added to an open stack view by selecting the
  "Add to focused viewer" option from the stacks menu. This allows multiple
  stacks to exist in the same view like overlays, while accounting for
  differences in translation and resolution. The navigator will expand the
  available zoom levels to accomodate the maximum and minimum zoom possible in
  all of the open stacks.
• Tile layers for stacks added to a viewer can be removed from a viewer via an
  "x" in the tile layer control.
• Multiple viewers into the same stack can now be opened.
• Each stack viewer can be toggled between coupling its navigation with other
  open stack viewers. Toggle this via the "Navigate with project" checkbox in
  the tile layer control.

Tile layer:

• New filter (WebGL only): intensity thresholded transparency

3D Viewer:

• Connector restriction can now explicitly be turned on and off with a pull
  down list. One can select between "Show all" (i.e. restriction turned off),
  "All shared connectors" will only show connectors with partners in the current
  selection and "All pre->post connectors" will only allow connectors with at
  least one presynaptic partner and one postsynaptic partner in the current
  selection. The last option, "All group shared" allows to select two skeleton
  sources (e.g. two selection table) and it will only show connectors that are
  part of the 3D viewer and that connect between both selected groups of
  skeletons. There is also a pre->post enforcing variant of it.

Neuron search:

• The name displayed for neurons now follows the same naming mechanism used for
  other widgets. It can be controlled through the settings widget and will
  automatically update if a neuron name is changed.

Miscellaneous:

• In the connectivity widget, upstream and downstream thresholds can now be set
  at once for all seed neurons. Two drop down controls used for this will be
  displayed if there is more than one seed neuron.
• Treenode Table refurbishing: far faster, supports multiple skeletons, can do
  tag search with regular expressions and lists the skeleton treenode ID.
• Rows and columns of the connectivity matrix can now be moved around with
  little buttons that appear when the mouse is over row and column header cells.
• There are now three options to change focus if a pointer enters a window:
  don't change focus (how it has been so far), focus stacks (will activate
  stacks when hovered, but won't change focus for other windows) and focus all
  (will change focus to every window hovered). The default will be stack focus
  follows the pointer. The settings widget makes these options available in
  general settings area.
• There are three new controls in the split/merge dialog: Toggle the
  display of input and output markers on neurons in the embedded 3D viewer and
  select which shading method is used (default: "active node split").
  Alternatively, "Strahler index" coloring can be used, which helps with
  depth perception.
• Attempting to reload a CATMAID browser tab or go back in history, will now
  result in a warning dialog, asking for confirmation. It makes clear that
  CATMAID's window layout and content won't be saved if the acton isn't
  canceled.

Administration:

• Now that virtual nodes are available, existing database can (but don't have
  to) be optimized. A new management command will look for straight skeleton
  parts that are not referenced in any way and prunes them. In other words, if
  there are three successive collinear nodes and the middle one is not
  referenced, it will be removed.

  manage.py catmaid_prune_skeletons

Bug fixes

• The Neuron Search widget doesn't throw an error anymore when a neuron listed
  in it is merged.
• There is no longer a race condition in the database during concurrent
  split/merge of a skeleton and creation of a treenode in that skeleton. While
  this is not a comprehensive guarantee of conflict-free concurrency, it does
  remove the most likely scenario resulting in corruption of the database model.