Open RandallJEllis opened 1 year ago
Would you be able to send me a folder with a subset of the raw TIF files? Also, what region and indicator/sensor are you imaging? That'll help me get a sense for what it should look like and anything that might need to be changed.
I can also get back with a line or two of code to load and save TIFF file series as a HDF5 using ciatah functions if that helps.
Hi Biafra,
Would you be able to send me a folder with a subset of the raw TIF files? Also, what region and indicator/sensor are you imaging? That'll help me get a sense for what it should look like and anything that might need to be changed.
Just emailed you a tar.gz of the first 100 frames because it was too big to attach here. The indicator is gcamp6f, and the data are from tumor spheroids, not in the brain.
I can also get back with a line or two of code to load and save TIFF file series as a HDF5 using ciatah functions if that helps.
Would definitely appreciate you sending this! Thank you!
Best,
Randy
I am getting cell segmentations that look pretty bad, and I think it might be because of how I am preparing the videos. Screenshots of the cell segmentations on the raw bigTIFF video and the preprocessed (downsampled 4x, turbo-reg'd, dfof) video are below:
Raw:![raw_movie](https://user-images.githubusercontent.com/7551835/227631637-944e51ac-e6c6-4e39-9b52-90bbc7346d74.PNG)
Pre-processed![dfof_movie](https://user-images.githubusercontent.com/7551835/227631654-295327b1-28e9-4864-9f75-8c86de510243.PNG)
I think the problem might be how I am preparing the bigTIFF video. The video is prepared from TIF images using the following script:
Any help with this is greatly appreciated. Thanks in advance!