sofima-testing

Sofima testing code.

Environment Setup:

Create a VM with preinstalled CUDA 11.3 drivers. This will save you a lot of work.
Run sofima_env.sh:

chmod u+x sofima_env.sh
./sofima_env.sh

Upload compatible cuDNN package, run sofima_cudnn.sh: Comaptible cuDNN package: cudnn-linux-x86_64-8.9.0.131_cuda11-archive.tar.xz

chmod u+x sofima_cudnn.sh
./sofima_cudnn.sh

Environment setup is a bash script because exporting a env.yml does not work. (breaks on environment creation due to pip dependency conflicts)

Name		Name	Last commit message	Last commit date
Latest commit History 54 Commits
connectomics		connectomics
.gitignore		.gitignore
README.md		README.md
aind_sofima_debug.ipynb		aind_sofima_debug.ipynb
cloud_utils.py		cloud_utils.py
coarse_reg_6_tiles.ipynb		coarse_reg_6_tiles.ipynb
coarse_registration.py		coarse_registration.py
config.py		config.py
config.yml		config.yml
data_prep.py		data_prep.py
exaspim_12_tiles.ipynb		exaspim_12_tiles.ipynb
fine_reg_6_tiles.ipynb		fine_reg_6_tiles.ipynb
fine_registration.py		fine_registration.py
full_sofima.ipynb		full_sofima.ipynb
full_sofima_refactor.ipynb		full_sofima_refactor.ipynb
fuse_and_multiscale.py		fuse_and_multiscale.py
fusion.py		fusion.py
fusion_6_tiles.ipynb		fusion_6_tiles.ipynb
fusion_multiscale_env.sh		fusion_multiscale_env.sh
fusion_rechunking.ipynb		fusion_rechunking.ipynb
multiscale.ipynb		multiscale.ipynb
multiscale.py		multiscale.py
multiscale_blocked_writer.py		multiscale_blocked_writer.py
multiscale_env.sh		multiscale_env.sh
ng_utils.py		ng_utils.py
quick_inital_alignment.ipynb		quick_inital_alignment.ipynb
register_a_dataset.py		register_a_dataset.py
sandbox_dispim.ipynb		sandbox_dispim.ipynb
sandbox_exaspim.ipynb		sandbox_exaspim.ipynb
sofima_cudnn.sh		sofima_cudnn.sh
sofima_env.sh		sofima_env.sh
test.ipynb		test.ipynb
tmp.ipynb		tmp.ipynb
tmp2.ipynb		tmp2.ipynb
tmp_fusion_log.txt		tmp_fusion_log.txt
tmp_fusion_log2.txt		tmp_fusion_log2.txt
workflow_coarse_reg.ipynb		workflow_coarse_reg.ipynb
workflow_fine_reg.ipynb		workflow_fine_reg.ipynb
zarr_io.py		zarr_io.py
zarr_processor.py		zarr_processor.py