Annotations

One central way to organize neurons and other spatial data structures in CATMAID is to use text annotations. They can be added to neurons and to annotations themselves, allowing hierarchies and nomenclatures of annotations.

There are a few special annotations that CATMAID will interpret in a particular way. The most commonly one is likely the locked annotation. If present on a neuron, no part of the skeleton can be changed anymore. The section below will introduce more special annotations:

Annotations can be added in many places within CATMAID. Often times widgets contain an “Annotate” button. The active skeleton can be annotated using the F3 key. This dialog shows also the present annotations and allows to add meta-annotations, which are simply annotations on annotations. In order to do that, click on the “Click here to also add a meta annotation” text link. The Neuron Navigator widget is also a useful simple widget to see the annotations of the current neuron.

Special Annotations

The annotations below have meaning in some context within CATMAID. Whether they need to be applied to neurons or annotations is noted in the description.

locked

If present on neuron, no change in morphology is allowed anymore.

stable

If present on neuron, during a join, the back-end will enforce that it is the winner in the join, i.e. its ID remains. If both join partners have this annotation, the join is canceled. This annotation can be configured through the Settings Widget for users with can_administer permissions on a project. Only the project/instance level config is respected by the back-end.

export: annotations

If present on a “publication annotation”, it is interpreted by the exporter to export annotations for the respective set of neurons, grouped by the publication annotation.

export: no-annotations

If present on a “publication annotation”, it is interpreted by the exporter to not export annotations for the respective set of neurons, grouped by the publication annotation.

export: tags

If present on a “publication annotation”, it is interpreted by the exporter to export tags for the respective set of neurons, grouped by the publication annotation.

export: no-tags

If present on a “publication annotation”, it is interpreted by the exporter to not export tags for the respective set of neurons, grouped by the publication annotation.

export: intra-connectors-only

If present on a “publication annotation”, it is interpreted by the exporter to export only the connectors linking between the members of the respective set of neurons, grouped by the publication annotation.

export: intra-connectors-and-placeholders

If present on a “publication annotation”, it is interpreted by the exporter to export only the connectors linking between the members of the respective set of neurons, grouped by the publication annotation. Additionally placeholder nodes with random IDs and data will be exported to reflect additional connections.

export: intra-connectors-and-original-placeholders

If present on a “publication annotation”, it is interpreted by the exporter to export only the connectors linking between the members of the respective set of neurons, grouped by the publication annotation. Additionally placeholder nodes with the original IDs and data will be exported to reflect additional connections.

export: no-connectors

If present on a “publication annotation”, it is interpreted by the exporter not to export connectors linking between the members of the set of neurons grouped by the publication annotation.