GSoC Project Idea 6.2: Improve accessibility and interactivity for datasets in CATMAID

This part of the project aims at ensuring that that the datasets converted in (1) are as accessible, visualizable and queryable as possible. This will mean making some contributions to the CATMAID development possibly both in the front-end (with JavaScript) and backend/API (in Python). Before this phase of the project starts, we will prioritize the feature requests. Some ideas or features, that have already been implemented to some degree:

  • Improve mesh support, including for instance deriving meshes from label volumes, superimpose mesh cross-sections on image data and add more visualization and query options to CATMAID’s 3D Viewer.
  • Persistence of the user interface, e.g. by extending CATMAID’s existing layout storage mechanisms to also include the data loaded in individual widgets, stack visualisations. One goal would be to be able to share a link with someone that might show an interesting circuit finding (e.g. showing a set of neurons in some widgets), including a comment.
  • Improve and/or work on missing issue for (label) volume support, as discussed in issues 1765 or 1801 (Notice the high issue number).

Skills required: Python, JavaScript, Git/GitHub, Adherence to code quality and review standards

Mentors: Stephan Gerhard, Zurich, Switzerland. Tom Kazimiers (main CATMAID developer), Janelia, US.

Links :

I might be able to help…how can I begin? I’ve the skillset which is required for this project