Open scharlottej13 opened 2 years ago
Brief comments:
Note: the napari plugin accelerator grant program is 6 months, which is why many projects have release dates targeted for June 2022. I guess it's possible CZI might do some no cost grant extensions, but for best results interacting with these groups in the first half of this year would be most productive.
Hi @scharlottej13, thanks for this writeup and pleased to meet you! I agree with @GenevieveBuckley's comments; zarpaint in particular relies on writing to bigger-than-RAM arrays, so it's not well suited to dask at the moment. @abigailmcgovern is working on using the painted arrays to train pytorch networks, and that could work very well with dask.
Re skan, a lot of the work that @GenevieveBuckley and I did might be obsolete soon thanks to a brand new, NumPy-only way to create graphs, which is in skan main branch and which is copied wholesale from this PR to scikit-image. I haven't played around yet with whether dask works out of the box with this approach but it seems to me like it should be easier than the numba-based approach from earlier.
@AbigailMcGovern is working on using the painted arrays to train pytorch networks, and that could work very well with dask.
Ooh yeah, this would be a great project for Dask engagement.
Background
Napari, an open-source tool for browsing, annotating, and analyzing large multi-dimensional images, is already well-integrated with Dask and was one of the projects @GenevieveBuckley focused on during her year as a Dask life science fellow (more background on that here). One area for improvement Genevieve noted, was for better integration with Dask early on in project development, which was the impetus for me joining CZI’s napari Plugin Accelerator Kickoff in December 2021. Here are a few projects I think could be relevant for integrating with Dask.
Juan Nunez-Iglesias @ Monash University
Chris Havlin @ University of Illinois
Virginie Uhlmann @ European Bioinformatics Institute