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Release 2021.12.21
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‎API_CHANGELOG.md

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through Swagger. Changes to undocumented, internal CATMAID APIs are not
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included in this changelog.
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## Under development
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## 2021.12.21
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### Additions
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‎CHANGELOG.md

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## Under development
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## 2021.12.21
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Contributors: Chris Barnes, Albert Cardona, Andrew Champion, Stephan Gerhard, Sanja Jasek, Tom Kazimiers
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### Notes
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‎django/projects/mysite/utils.py

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

‎sphinx-doc/source/_static/api/index.html

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‎sphinx-doc/source/_static/api/openapi.json

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

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

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

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

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

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

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

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

‎sphinx-doc/source/conf.py

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

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