Methods to stitch a position grid #137
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Big job! Looks great. I like the slurm job dependencies.
I'm in the middle of recreating your 2024_03_05_registration_test/live/3-stitch/ (~20% through the final step filling the last store) and everything's going smoothly.
Here are the small snags I've run into:
--slurmparameter tripped me up on thestitchcall. Seems required, so I suggest dropping it for now?- the default
--temp-dirwasn't writeable for me. Default to./? - When I open the stitched zarr in napari I get
GL_MAX_TEXTURE_SIZE 16384 in at least one axis and will be downsampled., and the viewable resolution is noticeably worse than the originals. Do we need pyramids? Another trick? I don't think this needs to block this merge, though.
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Thanks for your review @talonchandler! I implemented your suggestions for
That's true - so far this only happens for our largest (OPS) datasets and it hasn't bothered me much. It'll be nice to have a proper fix, which I think is implementing pyramids. This is not a blocker for now - analysis still happens on a FOV basis and detailed inspection can be done on smaller ROIs by loading a selection of the data through python. |
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LGTM! Thanks @ieivanov. |
She is ready!
This PR adds methods to stitch a grid of positions. Stitch parameters are computed with
>>> mantis estimate-stitch. Images are then stitched with>>> mantis stitch. Image registration parameters are computed on pairs of images using phase cross-correlation; the pipeline can be extended to include more complex transformations. The image mosaic is compiled using "average" blending; other blending modes may be implemented later.See examples in
/hpc/projects/intracellular_dashboard/ops/2024_03_05_registration_test/live/3-stitch/and/hpc/projects/intracellular_dashboard/ops/2024_04_11_Manual_HELA/1-stitch/v3/Replaces #135
See #135 (comment)
TODO:
compute_image_translationto CLI and save in config file