nd2totif-maskembryos-stagebin-pipeline

embryo images python pipeline

Project: Mechanism of transcription repression by an X-specific condensin in C. elegans"

Pipeline to analyse embryo images on the cluster. Some of the scripts can be used individually.

Scripts:

Checks for new nd2 files (by name pattern) on the server and trasnfer to the analysis server.
Convert nd2 to tif, and add metadata to csv.
Predict embryo masks with stardist.
Create individual embryo's cropped image, mask image and preview image (for manual insection).
Run stage prediction.
Add imagej metadata - so that images will open with channel seperation.
Copy all images and csv to data server.

Name		Name	Last commit message	Last commit date
Latest commit History 39 Commits
0_copy_to_scratch.py		0_copy_to_scratch.py
1_nd2_to_tif.py		1_nd2_to_tif.py
2_stardist_predict.py		2_stardist_predict.py
3_make_masked_embryos_and_previews.py		3_make_masked_embryos_and_previews.py
4_stage_prediction.py		4_stage_prediction.py
5_fix_tif_metadata_imagej_to_have_channels.ijm		5_fix_tif_metadata_imagej_to_have_channels.ijm
6_copy_to_data.py		6_copy_to_data.py
README.md		README.md
bad_missing_masks.txt		bad_missing_masks.txt
channel_to_channel_type.csv		channel_to_channel_type.csv
embryos.csv		embryos.csv
environment.yml		environment.yml
failing_nd2toTiff_files_also_imagej.txt		failing_nd2toTiff_files_also_imagej.txt
failing_nd2toTiff_files_and_rejected.txt		failing_nd2toTiff_files_and_rejected.txt
make_new_preview_images_with_two_fish_channels.py		make_new_preview_images_with_two_fish_channels.py
manually_inspect_masks_widget.ipynb		manually_inspect_masks_widget.ipynb
mask_correction_qsub_run.sh		mask_correction_qsub_run.sh
nd2totif.ijm		nd2totif.ijm
pipeline.log		pipeline.log
qsub_run.sh		qsub_run.sh
run_pipeline.sh		run_pipeline.sh
stardist_predict_for_mask_correction.py		stardist_predict_for_mask_correction.py

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