RFC: New "format" to store custom annotation for a custom slicer application

In the context of the Cell Locator project, a Slicer-based custom application to manually aligning specimens to annotated 3D spaces, we developed a json-based format to store annotation.


Until now the format has been used internally to the application

The current cell-locator format is similar to the markup json format expect it removes/includes few additional properties.

See https://github.com/BICCN/cell-locator/blob/master/Documentation/AnnotationFileFormat.md#2020-09-18

Proposed plan

To support the reading/loading of annotation by other application, we are now considering the following:

  1. “standardizing” it by including version information and schema similarly to what we already do for the json file associated with markups (see markups-schema-v1.0.1.json)

  2. creating standalone python tool for converting between version and streamline batch migration

  3. ensure the application automatically convert older format to newer ones.


  • Should we consider building on existing format or standard ?
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This is a very timely question. There are similar efforts around dicom SR encodings of annotations and quantitative results which may share some interests but maybe not others. Doing something application-specific is easiest to maintain of course, but I would love to see it standardized.