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Author: shntnu

assets/create_starrynight_example.sh

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+
+BUCKET=XXXXXX
+PROJECT=XXXXXX
+BATCH=XXXXXX
+
+export S3_PATH="s3://${BUCKET}/projects/${PROJECT}/${BATCH}"
+
+# Inputs
+
+## SBS images
+
+parallel mkdir -p scratch/starrynight_example/Source1/Batch1/images/Plate1/20X_c{1}_SBS-{1}/ ::: 1 2 3 4 5 6 7 8 9 10
+
+parallel --match '.*' --match '(.*) (.*) (.*)' \
+    aws s3 cp "${S3_PATH}/images/Plate1/20X_c{1}_SBS-{1}/Well{2.1}_Point{2.1}_{2.2}_ChannelC,A,T,G,DAPI_Seq{2.3}.ome.tiff" \
+    "scratch/starrynight_example/Source1/Batch1/images/Plate1/20X_c{1}_SBS-{1}/" ::: \
+    1 2 3 ::: \
+    "A1 0000 0000" "A1 0001 0001" "A2 0000 1025" "A2 0001 1026" "B1 0000 3075" "B1 0001 3076"
+
+## Cell Painting images
+
+mkdir -p scratch/starrynight_example/Source1/Batch1/images/20X_CP_Plate1_20240319_122800_179
+
+parallel --match '(.*) (.*) (.*)' \
+   aws s3 cp "${S3_PATH}/images/Plate1/20X_CP_Plate1_20240319_122800_179/Well{1.1}_Point{1.1}_{1.2}_ChannelPhalloAF750,ZO1-AF488,DAPI_Seq{1.3}.ome.tiff" \
+   "scratch/starrynight_example/Source1/Batch1/images/Plate1/20X_CP_Plate1_20240319_122800_179/" ::: \
+   "A1 0000 0000" "A1 0001 0001" "A2 0000 1025" "A2 0001 1026" "B1 0000 3075" "B1 0001 3076"
+
+# Outputs
+
+## Illumination correction images
+
+mkdir -p scratch/starrynight_example/Source1/Batch1/illum/Plate1
+parallel \
+   aws s3 cp "${S3_PATH}/illum/Plate1/Plate1_Cycle{1}_Illum{2}.npy" "scratch/starrynight_example/Source1/Batch1/illum/Plate1/" ::: \
+   1 2 3 ::: \
+   DNA A T G C
+
+
+## Cell Painting images: Illumination corrected
+
+parallel \
+   aws s3 cp "${S3_PATH}/images_corrected/painting/Plate1-Well{1}/Plate_Plate1_Well_Well{1}_Site_{2}_Corr{3}.tiff" \
+   "scratch/starrynight_example/Source1/Batch1/images_corrected/painting/Plate1-Well{1}/" ::: \
+   A1 A2 B1 ::: 0 1 ::: DNA Phalloidin ZO1
+
+
+parallel \
+   aws s3 cp "${S3_PATH}/images_corrected/painting/Plate1-Well{1}/PaintingIllumApplication_{2}.csv" \
+   "scratch/starrynight_example/Source1/Batch1/images_corrected/painting/Plate1-Well{1}/" ::: \
+   A1 A2 B1 ::: Cells ConfluentRegions Experiment Image Nuclei
+
+# SBS images: Illumination aligned
+
+parallel \
+   aws s3 cp "${S3_PATH}/images_aligned/barcoding/Plate1-Well{1}-{2}/Plate_Plate1_Well_{1}_Site_{2}_Cycle0{3}_{4}.tiff" \
+   "scratch/starrynight_example/Source1/Batch1/images_aligned/barcoding/Plate1-Well{1}-{2}/" ::: \
+   A1 A2 B1 ::: 0 1 ::: 1 2 3 ::: A T G C DAPI
+
+
+parallel \
+   aws s3 cp "${S3_PATH}/images_aligned/barcoding/Plate1-Well{1}-{2}/BarcodingApplication_{3}.csv" \
+   "scratch/starrynight_example/Source1/Batch1/images_aligned/barcoding/Plate1-Well{1}-{2}/" ::: \
+   A1 A2 B1 ::: 0 1 ::: Experiment Image
+
+## SBS images: Illumination corrected
+
+parallel \
+   aws s3 cp "${S3_PATH}/images_corrected/barcoding/Plate1-Well{1}-{2}/Plate_Plate1_Well_{1}_Site_{2}_Cycle0{3}_{4}.tiff" \
+   "scratch/starrynight_example/Source1/Batch1/images_corrected/barcoding/Plate1-Well{1}-{2}/" ::: \
+   A1 A2 B1 ::: 0 1 ::: 1 2 3 ::: A T G C
+
+parallel \
+   aws s3 cp "${S3_PATH}/images_corrected/barcoding/Plate1-Well{1}-{2}/Plate_Plate1_Well_{1}_Site_{2}_Cycle0{3}_{4}.tiff" \
+   "scratch/starrynight_example/Source1/Batch1/images_corrected/barcoding/Plate1-Well{1}-{2}/" ::: \
+   A1 A2 B1 ::: 0 1 ::: 1 ::: DAPI
+# DAPI is only present in the first cycle
+
+
+parallel \
+   aws s3 cp "${S3_PATH}/images_corrected/barcoding/Plate1-Well{1}-{2}/BarcodePreprocessing_{3}.csv" \
+   "scratch/starrynight_example/Source1/Batch1/images_corrected/barcoding/Plate1-Well{1}-{2}/" ::: \
+   A1 A2 B1 ::: 0 1 ::: BarcodeFoci PreFoci Experiment Image Nuclei
+
+## Segmentation images
+
+parallel \
+   aws s3 cp "${S3_PATH}/images_segmentation/Plate1/Plate_Plate1_Well_Well{1}_Site_{2}_Corr{3}_SegmentCheck.png" \
+   "scratch/starrynight_example/Source1/Batch1/images_segmentation/Plate1/" ::: \
+   A1 A2 B1 ::: 0 ::: DNA
+# Notice the odd naming of Well
+
+parallel \
+   aws s3 cp "${S3_PATH}/images_segmentation/Plate1/Plate_Plate1_Well_Well{1}_Site_{2}_Corr{3}_SegmentCheck.png" \
+   "scratch/starrynight_example/Source1/Batch1/images_segmentation/Plate1/" ::: \
+   A1 A2 B1 ::: 0 ::: DNA
+
+parallel \
+   aws s3 cp "${S3_PATH}/images_segmentation/Plate1/SegmentationCheck_{1}.csv" \
+   "scratch/starrynight_example/Source1/Batch1/images_segmentation/Plate1/" ::: \
+   Experiment Image Nuclei Cells PreCells ConfluentRegions
+
+
+## Load Data CSVs
+
+export S3_PATH_WORKSPACE="s3://${BUCKET}/projects/${PROJECT}/workspace"
+
+aws s3 sync \
+   "${S3_PATH_WORKSPACE}/load_data_csv/${BATCH}/Plate1/" \
+   "scratch/starrynight_example/Source1/workspace_example/load_data_csv/Batch1/Plate1/"
+
+
+## Analysis CSVs
+
+parallel \
+   aws s3 sync \
+   "${S3_PATH_WORKSPACE}/analysis/${BATCH}/Plate1-Well{1}-{2}/" \
+   "scratch/starrynight_example/Source1/workspace_example/analysis/${BATCH}/Plate1-Well{1}-{2}/" \
+   --exclude \""*.csv\"" ::: \
+   A1 A2 B1 ::: 0 1
+
+
+parallel \
+   aws s3 sync "${S3_PATH_WORKSPACE}/analysisfix/${BATCH}/Plate1-Well{1}-{2}/" \
+   "scratch/starrynight_example/Source1/workspace_example/analysis/${BATCH}/Plate1-Well{1}-{2}/" ::: \
+   A1 A2 B1 ::: 0 1