Release 2021.12.21

API_CHANGELOG.md

@@ -2,7 +2,7 @@ This changelog notes changes to API endpoints that are documented and listed
 through Swagger. Changes to undocumented, internal CATMAID APIs are not
 included in this changelog.
 
-## Under development
+## 2021.12.21
 
 ### Additions
 

CHANGELOG.md

@@ -1,5 +1,6 @@
-## Under development
+## 2021.12.21
 
+Contributors: Chris Barnes, Albert Cardona, Andrew Champion, Stephan Gerhard, Sanja Jasek, Tom Kazimiers
 
 ### Notes
 

django/projects/mysite/utils.py

@@ -9,11 +9,11 @@
 
 # This variable contains a reference version of the current code-base. It is
 # updated by release and dev-cycle scripts.
-BASE_VERSION = '2020.02.15-dev'
+BASE_VERSION = '2021.12.21'
 # This commit is the reference commit of the BASE_VERSION above. Technically, it
 # is the commit right before the BASE_VERSION, because the release script will
 # change these fields and onlt create the actual release commit after the changes.
-BASE_COMMIT = 'e8e89cdc441ae20e0f7217578ca98d03074b6b8e'
+BASE_COMMIT = '5e2c7a82890fe274291b231e5ae0ea3491d7d8c1'
 # These file is created as part of our Docker build and is looked at as
 # fall-back, should no git environment be available. The VERSION_INFO_PATH file
 # contains the "git describe" output of the build environment.

sphinx-doc/source/_static/widgets/analyse-arbor.html

@@ -0,0 +1,42 @@
+<p>
+The <em>Analyze Arbor</em> widget shows different statistics on whole neurons
+and different parts of them. Its working set of skeletons is shown in the table
+at the top, which skeletons can be added to or removed from through the source
+selector and buttons like <em>Append</em> in the widget toolbar, like it is the
+case with many widgets.
+</p>
+
+<p>
+This table is divided into information on four different views on a neuron,
+which are determined by CATMAID automatically by assuming the root node of a
+skeleton is at its soma and the end of visible microtubules are marked using the
+<em>microtubules end</em> tag. The neuron's axonic and dendritic parts are
+determined using flow centrality (FC). If no axon terminals can be determined
+through synapse clustering and FC, dendrites will be considered everything not
+part of the backbone (see below):
+<ol>
+  <li><em>Arbor:</em> this is the entire skeleton</li>
+  <li><em>Backbone:</em> all nodes reachable from the root node until a
+    "microtubules end" tag is found</li>
+  <li><em>Dendrites:</em> the dendritic nodes according to FC, usually most of
+    inputs. If FC finds no cut, dendrites will be all nodes not in backbone</li>
+  <li><em>Axon terminals:</em> the axon as determined by FC, usually most
+    outputs. If FC finds no cut, no axon terminals will be analyzed explicitly.</li>
+</ol>
+</p>
+<p>
+For each of those a set of statistics is listed:
+<ol>
+  <li><em>Cable (nm):</em>: the total length of the respective part, Gaussian
+    smoothed with a sigma of 200 nm</li>
+  <li><em>Inputs:</em> the number of postsynaptic sites</li>
+  <li><em>Outputs:</em> the number of presynaptic sites</li>
+  <li><em>Time (min):</em> the number of minutes in which nodes have been
+    created in this part</li>
+  <li><em>Mitochondria:</em> The number of nodes tagged with "mitochondrium" in
+    this part</li>
+</ol>
+</p>
+
+<p>The second part of the widget visualizes various histograms and statistics
+for each part.

sphinx-doc/source/_static/widgets/link-widget.html

@@ -0,0 +1,41 @@
+<p>
+This widget allows users to create persistent deep links into the dataset using
+an alias. This alias needs to be unique per project. The link table in the first
+tab will only list links that are marked as visible to others who have access to
+the project. Links marked as private, are only visible and accessible by the
+creator of the link.
+</p>
+
+<p>
+The stored parameters are the same as for regular deep links, with
+most of them being optional, including the widget layout, widget settings and
+loaded skeletons. The widget tab to add links allows to configure these options
+in the tab button panel. By default the Link Widget itself is ignored when
+storing layouts, which can of course be changed as well.
+
+<p>
+The alias defined for a link can be used to open the deep link, either by using
+the link presented in the widget (the Alias column):
+</p>
+
+<p class="inline-code">
+&lt;catmaid-url&gt;/&lt;project-id&gt;/links/&lt;alias&gt;
+</p>
+
+<p>
+which is only an internal redirect to
+</p>
+
+<p class="inline-code">
+&lt;catmaid-url&gt;?pid=&lt;project-id&gt;&link=&lt;alias&gt;
+</p>
+
+<p>
+but looks friendlier. Moreover links can be marked private, making them
+only accessible (and listable) by the creator of the link.
+</p>
+
+<p>
+An optional message can be stored with the link and is shown to the user when
+the links is opened.
+</p>

sphinx-doc/source/_static/widgets/morphology-plot.html

@@ -0,0 +1,48 @@
+<h1>Morphology Plot</h1>
+<p>
+  This widget is a histogram based analysis tool which provides information on
+  nodes with a similar distance to a reference location, which can be a specified
+  in the user interface.  Example choices are the root node or the average node
+  position. Around this center, spheres are formed with an increasing radius that
+  can be defined by the user and defaults to 1000nm per step. All nodes within the
+  part of a sphere that doesn\'t overlap with the last smaller sphere is treated
+  as one bin of a histogram. This is shown for three bins in 2D below:</p>
+<p>
+  <svg height="100" with="100" viewBox="0 0 100 100" xmlns="http://www.w3.org/2000/svg">
+    <circle cx="50" cy="50" r="49" style="stroke: #000; fill: #fff"/>
+    <circle cx="50" cy="50" r="30" style="stroke: #000; fill: #fff"/>
+    <circle cx="50" cy="50" r="10" style="stroke: #000; fill: #fff"/>
+    <text x="50" y="53" style="font-size: 10px; text-anchor: middle">1</text>
+    <text x="31" y="53" style="font-size: 10px; text-anchor: middle">2</text>
+    <text x="10" y="53" style="font-size: 10px; text-anchor: middle">3</text>
+  </svg>
+</p>
+<p>
+  Which nodes are part of which bin depends heavily on the morphology of a
+  neuron. The widget allows then to compute various metrics on those bins:
+  <ul>
+    <li><b>Sholl analysis:</b> The number of edges intersecting with the boundary
+      of the smaller sphere. Notice that if parent-child segments are longer than
+      radius-increment in the radial direction, some parent-child segments will be
+      counted more than once, which is correct.</li>
+    <li><b>Radial density of cable:</b> Approximate aggregated cable length per
+      bin by adding the length of all child-parent edges of all child nodes in the
+      bin.</li>
+    <li><b>Radial density of branch nodes:</b>The number of branch nodes in a
+      particular bin.</li>
+    <li><b>Radial density of ends:</b> The number of end nodes in a particular
+      bin.</li>
+    <li><b>Radial density of input synapses:</b> The number of input synapses in
+      a particular bin.</li>
+    <li><b>Radial density of output synapses:</b> The number of output synapses
+      in a particular bin.</li>
+    <li><b>Radial density of gap junctions:</b> The number of gap junctions in a
+      particular bin.</li>
+    <li><b>Radial density of desmosomes:</b> The number of desmosomes in a
+      particular bin.</li>
+  </ul>
+</p>
+<p>
+  The plot itself shows the distance from the selected center on the X axis and
+  the bin value (e.g. the number of end nodes) is shown on the Y axis.
+<p>

sphinx-doc/source/_static/widgets/publication-widget.html

@@ -0,0 +1,12 @@
+<p>
+  The central table displays all known publications. These are representated as
+  annotatiosn that are themselves annotaed with one of the defined <em>publication
+  annotations</em>, they can be configured in the Settings Widget and amount by
+  default to to <em>Published, papers, paper</em>. The widget allows to create
+  new publications and configure the export options for each publication. The
+  export options can either be defined explicitly for each publication (asterisk
+  is gray) or the project-wide defaults can be used (asterisk is orange).
+  Clicking the check-mark icon will always go into per-publication mode and
+  explicitly set the export option. Clicking the asterisk enables inherit-mode
+  again.
+</p>

sphinx-doc/source/conf.py

@@ -55,9 +55,9 @@
 # built documents.
 #
 # The short X.Y version.
-version = '2020.02.15-dev'
+version = '2021.12.21'
 # The full version, including alpha/beta/rc tags.
-release = '2020.02.15-dev'
+release = '2021.12.21'
 # The language for content autogenerated by Sphinx. Refer to documentation
 # for a list of supported languages.
 #language = None