Use MM to create BrainGlobe Atlas API compatible packaged atlases

[adamltyson]

Following an earlier discussion this is to track the idea of adapting MM to allow for the creation and packaging of BG atlases. This could be useful for:

• Creation of new atlases from existing data (e.g. 2D -> 3D)
• Refinement of existing atlases (e.g. adding a new region)
• Creation of new atlases from raw data

As far as I'm aware most of the functionality is already there for smoothing etc, but what is needed would be:

• A GUI to package up the atlases, and ideally create a script that can be run headlessly (like the existing atlas generation scripts.
• Capability to load various file formats
• .....

[yoda-vid]

Excited to work on this together! Thanks for organizing, @adamltyson. Would be great to leverage these tools for one another and expand interoperability.

GUI access to existing BG atlases and locally generated ones is almost ready in #75. I'll need to streamline notifications on download status. Always open to adding in more functionality, too.

It would be great to build on the excellent GUI work that @pr4deepr started for package generation. Perhaps we could keep it modular it so that it would work both within MM and independently of it, and in either case to produce a script for headless generation. After building the atlas, one could test it in MM to check for proper orientation, resolutions, etc.

Currently, MM uses SimpleITK to load various medical imaging formats, Bio-Formats to import other microscopy formats, and recent (limited) support for Tifffile to load TIFFs directly when possible. It would help to see if this meets folks' needs and also any bottlenecks in using them.

For atlas creation or extension to new regions, I would love to expand the annotation tools to help atlas authors. Basic drawing/painting is supported along with a 3D interpolation tool so far. I could envision people building/refining atlases, packaging them up for BG, testing/iterating on them, and posting to BG for others to download from MM or their tool of choice!

[adamltyson]

@chaplinta, @simonweiler, this is the effort I mentioned on slack. Would an atlas refinement/packaging GUI be useful for you?