Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Cropping MERFISH image is slow when subsetting #65

Closed
lambdamoses opened this issue Feb 5, 2025 · 0 comments
Closed

Cropping MERFISH image is slow when subsetting #65

lambdamoses opened this issue Feb 5, 2025 · 0 comments

Comments

@lambdamoses
Copy link
Collaborator

I got this complaint a few times, so I'm opening an issue to let users know that I'm fixing it. Basically the problem is that SFE crops the image to the new bounding box when the SFE object is subsetted as part of the spatial subsetting, but MERFISH images are often like 20GB so if you're only removing a small fraction of cells in QC, the cropping is really slow. I'll add an option to skip cropping. If the output file is larger than a threshold, then a message will be printed saying skip cropping, but that threshold can be changed with options().

lambdamoses added a commit that referenced this issue Feb 11, 2025
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Labels
None yet
Projects
None yet
Development

No branches or pull requests

1 participant