GitHub - snownontrace/Sekiguchi-et-al-2022

This repo contains all scripts used for data analysis in Sekiguchi et al., 2022, JDR.

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Name		Name	Last commit message	Last commit date
Latest commit History 2 Commits
README.md		README.md
SMG-Col4-BM-linescan-sg-Serpinh1.ipynb		SMG-Col4-BM-linescan-sg-Serpinh1.ipynb
SMG-a3integrin-linescan-sg-Itga9-grouped.ipynb		SMG-a3integrin-linescan-sg-Itga9-grouped.ipynb
SMG-a3integrin-linescan-sg-Itga9.ipynb		SMG-a3integrin-linescan-sg-Itga9.ipynb
SMG-a6integrin-BM-linescan-sg-Itga9.ipynb		SMG-a6integrin-BM-linescan-sg-Itga9.ipynb
SMG-a6integrin-linescan-sg-Itga9-grouped.ipynb		SMG-a6integrin-linescan-sg-Itga9-grouped.ipynb
SMG-a6integrin-linescan-sg-Itga9.ipynb		SMG-a6integrin-linescan-sg-Itga9.ipynb
SMG-a9integrin-linescan-plotting.ipynb		SMG-a9integrin-linescan-plotting.ipynb
SMG-b1integrin-linescan-E16.ipynb		SMG-b1integrin-linescan-E16.ipynb
SMG-b1integrin-linescan-plotting.ipynb		SMG-b1integrin-linescan-plotting.ipynb
SMG-b1integrin-linescan-time-course.ipynb		SMG-b1integrin-linescan-time-course.ipynb
SMG-bud-count-Itga9-Rei-Kaz.ipynb		SMG-bud-count-Itga9-Rei-Kaz.ipynb
SMG-bud-count-Itgb1-plate-i-Rei-Kaz.ipynb		SMG-bud-count-Itgb1-plate-i-Rei-Kaz.ipynb
SMG-bud-count-Itgb1-time-course-Rei-Kaz.ipynb		SMG-bud-count-Itgb1-time-course-Rei-Kaz.ipynb
SMG-bud-count-Serpinh1-Rei-Kaz.ipynb		SMG-bud-count-Serpinh1-Rei-Kaz.ipynb
SMG-bud-count-culture-conditions.ipynb		SMG-bud-count-culture-conditions.ipynb
SMG-bud-count-decoding-plotting-211022-25.ipynb		SMG-bud-count-decoding-plotting-211022-25.ipynb
SMG-bud-count-plateI-E16-Itgb1-Rei-Kaz.ipynb		SMG-bud-count-plateI-E16-Itgb1-Rei-Kaz.ipynb
SMG-bud-count-plateII-E16-Itgb1-Rei-Kaz.ipynb		SMG-bud-count-plateII-E16-Itgb1-Rei-Kaz.ipynb
SMG-epi-HSP47-get-mean-intensity.ijm		SMG-epi-HSP47-get-mean-intensity.ijm
SMG-epi-HSP47-mean-intensity-plotting.ipynb		SMG-epi-HSP47-mean-intensity-plotting.ipynb
SMG-epi-blasticidin-Cellpose-segmentation.ipynb		SMG-epi-blasticidin-Cellpose-segmentation.ipynb
SMG-epi-blasticidin-calc-ratio.ipynb		SMG-epi-blasticidin-calc-ratio.ipynb
SMG-epi-blasticidin-plot-Cellpose-outline-masks.ipynb		SMG-epi-blasticidin-plot-Cellpose-outline-masks.ipynb
SMG-epi-blasticidin-plot-ratios.ipynb		SMG-epi-blasticidin-plot-ratios.ipynb
SMG-epi-get-background-intensity.ijm		SMG-epi-get-background-intensity.ijm
SMG-epi-get-mean-intensity.ijm		SMG-epi-get-mean-intensity.ijm
SMG-get-Col4-BM-edge-AUC-peakHeight-by-line-scan.ijm		SMG-get-Col4-BM-edge-AUC-peakHeight-by-line-scan.ijm
SMG-get-a3-integrin-edge-AUC-peakHeight-by-line-scan.ijm		SMG-get-a3-integrin-edge-AUC-peakHeight-by-line-scan.ijm
SMG-get-a6-integrin-BM-edge-AUC-peakHeight-by-line-scan.ijm		SMG-get-a6-integrin-BM-edge-AUC-peakHeight-by-line-scan.ijm
SMG-get-a9-integrin-edge-AUC-peakHeight-by-line-scan-v1.ijm		SMG-get-a9-integrin-edge-AUC-peakHeight-by-line-scan-v1.ijm
SMG-get-a9-integrin-edge-AUC-peakHeight-by-line-scan-v2.ijm		SMG-get-a9-integrin-edge-AUC-peakHeight-by-line-scan-v2.ijm
SMG-get-b1-integrin-edge-AUC-peakHeight-by-line-scan.ijm		SMG-get-b1-integrin-edge-AUC-peakHeight-by-line-scan.ijm
bioformats-split-positions.ijm		bioformats-split-positions.ijm
countBuds.ijm		countBuds.ijm
countBudsMinProj.ijm		countBudsMinProj.ijm
fixed-images-general-190503-Col4-IF.ijm		fixed-images-general-190503-Col4-IF.ijm
fixed-images-general-190523-CRISPR-KO-SMG-IF.ijm		fixed-images-general-190523-CRISPR-KO-SMG-IF.ijm
fixed-images-general-20200129-0201-Cas9Tg-LV-188-317-318-401-410-411.ijm		fixed-images-general-20200129-0201-Cas9Tg-LV-188-317-318-401-410-411.ijm
fixed-images-general-20210104-Cas9Tg-LV-188-317-318-319-IF.ijm		fixed-images-general-20210104-Cas9Tg-LV-188-317-318-319-IF.ijm
fixed-images-general-210104-a9int-IF.ijm		fixed-images-general-210104-a9int-IF.ijm
fixed-images-general-210614-Cas9-SMGepi-anti-b1-integrin-60x-oil.ijm		fixed-images-general-210614-Cas9-SMGepi-anti-b1-integrin-60x-oil.ijm
fixed-images-general-220606-a3int-IF.ijm		fixed-images-general-220606-a3int-IF.ijm
fixed-images-general-220606-a6int-IF.ijm		fixed-images-general-220606-a6int-IF.ijm
fixed-images-general-220608-b1int-IF-E16-get-arguments.ijm		fixed-images-general-220608-b1int-IF-E16-get-arguments.ijm
fixed-images-general-220608-b1int-IF-time-course-get-arguments.ijm		fixed-images-general-220608-b1int-IF-time-course-get-arguments.ijm
fixed-images-general-220608-b1int-IF-time-course.ijm		fixed-images-general-220608-b1int-IF-time-course.ijm
fixed-images-general-phase-contrast-images.ijm		fixed-images-general-phase-contrast-images.ijm
hash_file_names.py		hash_file_names.py
hash_file_names_folders.py		hash_file_names_folders.py
makeMontageFromImageSequence-more-options.ijm		makeMontageFromImageSequence-more-options.ijm
makeMontageFromImageSequence.ijm		makeMontageFromImageSequence.ijm
meta-macro-folders.ijm		meta-macro-folders.ijm
nd2_to_tiff.ijm		nd2_to_tiff.ijm
qPCR-analysis-220519-plate1to3.ipynb		qPCR-analysis-220519-plate1to3.ipynb
qPCR-analysis-220519-plate3.ipynb		qPCR-analysis-220519-plate3.ipynb
qPCR-analysis-220525-plate1n2.ipynb		qPCR-analysis-220525-plate1n2.ipynb
qPCR-analysis-220525-plate3to5.ipynb		qPCR-analysis-220525-plate3to5.ipynb
qPCR-analysis-220606-plate1to3.ipynb		qPCR-analysis-220606-plate1to3.ipynb
qPCR-analysis-220613-plate1to5.ipynb		qPCR-analysis-220613-plate1to5.ipynb
qPCR-analysis-220627-plate1to2.ipynb		qPCR-analysis-220627-plate1to2.ipynb
qPCR-analysis-220627-plate3to5.ipynb		qPCR-analysis-220627-plate3to5.ipynb
qPCR-analysis-sg-Itga9-testing-Itga3-6.ipynb		qPCR-analysis-sg-Itga9-testing-Itga3-6.ipynb
qPCR-analysis-sg-Itga9.ipynb		qPCR-analysis-sg-Itga9.ipynb
qPCR-analysis-sg-Itgb1.ipynb		qPCR-analysis-sg-Itgb1.ipynb
qPCR-analysis-sg-Serpinh1-220519.ipynb		qPCR-analysis-sg-Serpinh1-220519.ipynb
qPCR-analysis-sg-Serpinh1.ipynb		qPCR-analysis-sg-Serpinh1.ipynb
reverse_hashed_file_names.py		reverse_hashed_file_names.py
reverse_order_file_names.py		reverse_order_file_names.py
run_cellpose.ipynb		run_cellpose.ipynb
spheroids-processing-phase-only.ijm		spheroids-processing-phase-only.ijm
sw_plotting.py		sw_plotting.py
sw_qPCR.py		sw_qPCR.py
sw_tracking.py		sw_tracking.py
sw_utilities.py		sw_utilities.py

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