donglab_workflows

Image registration workflows as part of Next Generation MORF BRAIN Initiative Project

Algorithms use GPU parallelization enabled by the pytorch library.

todo: finalize code into a series of scripts. include instructions for setting up vertual env with all requirements

need: required specifications for interfacing with necessary outputs.

Daniel's plan

start with jupyter notebooks, then turn them into scripts to be run by other users on a cluster.

Functions will move to an importable library.

This is in the twardlab organization, but can be forked elsewhere.

Name		Name	Last commit message	Last commit date
Latest commit History 69 Commits
pipeline_building		pipeline_building
.gitignore		.gitignore
README.md		README.md
Test.txt		Test.txt
donglab_workflows.py		donglab_workflows.py
downsample_workflows_scratch_v00.ipynb		downsample_workflows_scratch_v00.ipynb
downsample_workflows_scratch_v00a_MIT.ipynb		downsample_workflows_scratch_v00a_MIT.ipynb
downsample_workflows_scratch_v00b_hanpeng.ipynb		downsample_workflows_scratch_v00b_hanpeng.ipynb
downsample_workflows_scratch_v00c_morf4x.ipynb		downsample_workflows_scratch_v00c_morf4x.ipynb
dragonfly_atlas_reg_workflows_scratch_v04_deformslab.ipynb		dragonfly_atlas_reg_workflows_scratch_v04_deformslab.ipynb
dragonfly_reg_10_to_30_workflows_scratch_v00.ipynb		dragonfly_reg_10_to_30_workflows_scratch_v00.ipynb
example_loading_data_v00.ipynb		example_loading_data_v00.ipynb
lightsheet_reg_workflows_scratch_v03_local.ipynb		lightsheet_reg_workflows_scratch_v03_local.ipynb
lightsheet_reg_workflows_scratch_v03a_localMIT.ipynb		lightsheet_reg_workflows_scratch_v03a_localMIT.ipynb
lightsheet_reg_workflows_scratch_v03c_morf4x.ipynb		lightsheet_reg_workflows_scratch_v03c_morf4x.ipynb
notebookguivenv.sh		notebookguivenv.sh
requirements.txt		requirements.txt
simulated_cells_v00.ipynb		simulated_cells_v00.ipynb
stp_reg_workflows_scratch_v03b_hanpeng.ipynb		stp_reg_workflows_scratch_v03b_hanpeng.ipynb