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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().
The text was updated successfully, but these errors were encountered:
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()
.The text was updated successfully, but these errors were encountered: