Closed ieivanov closed 4 months ago
Thanks for your review @talonchandler! I implemented your suggestions for --temp-path
and --slurm
options. Let's merge this and we'll fix other issues through smaller PRs.
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.
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.
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 https://github.com/czbiohub-sf/shrimPy/pull/135#issuecomment-2038005161
TODO:
compute_image_translation
to CLI and save in config file