MultiModalBrowser

Dear forum users,

we would like to announce the MultiModalBrowser (MMB), a Fiji plugin to explore and analyse big image data from multiple modalities. The plugin was developed for a cellular atlas of Platynereis dumerilii we have recently published, but we envision it to be useful for similar data-sets and invite feedback and suggestions. It was mainly developed by @Christian_Tischer; I have contributed the data layout.

The MMB uses BigDataViewer to display image volumes and extends the functionality of BDV with the following features:

  • Support for browsing image data either stored locally in the bdv.hdf5 or bdv.n5 format as well as remotely from a s3 compatible object store.
  • User interface to easily select data from different modalities.
  • Support for displaying segmentation layers (based on functionality from Paintera).
  • Support for tabular data associated with segmentation objects and browsing, coloring and extending based on these tables.
  • Integration with the ImageJ 3D viewer to render segmentation objects and volumes in 3D.
  • Search for local image data in order to analyze images which are not linked to a segmentation yet.
  • Support for bookmarks that can restore the complete viewer state

In order to use it for your own data, a specific folder structure is needed. See this repository for a minimal example and a small python library with helper functions. You can find the full data for the Platynereis data-set here.

Any feedback or suggestions for additional features or usability are welcome. Also, let use know if you want to use the MMB for your own data and run into any issues.

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very interesting! I’ve been looking for this for a long time but in vain! Thank you so much

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