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update README for journal requirements
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@jjahanip
jjahanip authored and jjahanip committed Jul 13, 2020
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1 change: 1 addition & 0 deletions .gitignore
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Expand Up @@ -108,3 +108,4 @@ venv.bak/

# temp
temp.py
DETECTION/models/*
262 changes: 138 additions & 124 deletions README.md
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2 changes: 1 addition & 1 deletion RECONSTRUCTION/registration.py
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Expand Up @@ -491,7 +491,7 @@ def registration (input_dir,output_dir,target_round = "R2", imadjust = True,
paras.set_tile_shape([]) # no tiling, cautious might be extremely slow!

if os.path.exists(output_dir) is False:
os.mkdir(output_dir)
os.makedirs(output_dir)

# Set_name = os.listdir(args.input_dir)[1].split("_")[0] + "_"
input_dir_image = [f for f in os.listdir(input_dir) if f.endswith('.tif')]
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0 main_reconstruction_lin.py → main_reconstruction.py
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78 changes: 0 additions & 78 deletions main_reconstruction_win.py
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110 changes: 55 additions & 55 deletions scripts/reconstruction/50_plex.csv
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@@ -1,56 +1,56 @@
filename,biomarker,structure,intra channel correction,inter channel correction,channel 1,channel 2,channel 3,xmin,ymin,xmax,ymax
S1_R1C1.tif,DAPI,Nucleus,Yes,Yes,,,,2000,4000,15000,13000
S1_R1C10.tif,Cleaved Caspase-3,Cytoplasm,Yes,Yes,S1_R1C7.tif,S1_R1C4.tif,S1_R1C6.tif,2000,4000,15000,13000
S1_R1C11.tif,Phase Contrast Bright Field,Cell Morphology,No,No,,,,2000,4000,15000,13000
S1_R1C2.tif,Tyrosine Hydroxylase (TH),"Soma, Processes",Yes,Yes,S1_R1C1.tif,,,19000,18500,21000,19500
S1_R1C3.tif,Blood Brain Barrier,Plasma Membrane,Yes,Yes,,,,2000,4000,15000,13000
S1_R1C4.tif,GFP,Cytoplasm,Yes,Yes,,,,2000,4000,15000,13000
S1_R1C5.tif,Iba1,"Soma, Processes",Yes,Yes,,,,2000,4000,15000,13000
S1_R1C6.tif,RECA1,Plasma Membrane,Yes,Yes,,,,2000,4000,15000,13000
S1_R1C7.tif,Aquaporin-4,Plasma Membrane,Yes,Yes,S1_R1C4.tif,,,2000,4000,15000,13000
S1_R1C8.tif,Tomato Lectin,Plasma Membrane,Yes,Yes,,,,2000,4000,15000,13000
S1_R1C9.tif,Olig2,Nucleus,Yes,Yes,S1_R1C7.tif,S1_R1C4.tif,S1_R2C4.tif,2000,4000,15000,13000
S1_R2C1.tif,DAPI,Nucleus,Yes,Yes,,,,2000,4000,15000,13000
S1_R2C10.tif,Smooth Muscle Actin,"Soma, Processes",Yes,Yes,,,,2000,4000,15000,13000
S1_R2C11.tif,Phase Contrast Bright Field,Cell Morphology,No,No,,,,2000,4000,15000,13000
S1_R2C2.tif,Histones,Nucleus,Yes,Yes,,,,2000,4000,15000,13000
S1_R2C3.tif,PDGFR beta,Plasma Membrane,Yes,Yes,S1_R2C6.tif,,,2000,4000,15000,13000
S1_R2C4.tif,NeuN,Nucleus,Yes,Yes,,,,2000,4000,15000,13000
S1_R2C5.tif,Synaptohysin,Synapses,Yes,Yes,S1_R2C6.tif,,,2000,4000,15000,13000
S1_R2C6.tif,Parvalbumin,"Soma, Processes",Yes,Yes,,,,2000,4000,15000,13000
S1_R2C7.tif,Choline Acetyltransferase,"Soma, Processes",Yes,Yes,S1_R2C9.tif,S1_R2C4.tif,S1_R2C5.tif,28000,15400,36600,21200
S1_R2C8.tif,Tomato Lectin,Plasma Membrane,Yes,Yes,,,,2000,4000,15000,13000
S1_R2C9.tif,Glutaminase,"Soma, Processes",Yes,Yes,S1_R2C7.tif,,,2000,4000,15000,13000
S1_R3C1.tif,DAPI,Nucleus,Yes,Yes,,,,2000,4000,15000,13000
S1_R3C10.tif,Vimentin,Processes,Yes,Yes,,,,2000,4000,15000,13000
S1_R3C11.tif,Phase Contrast Bright Field,Cell Morphology,No,No,,,,2000,4000,15000,13000
S1_R3C2.tif,Histones,Nucleus,Yes,Yes,,,,2000,4000,15000,13000
S1_R3C3.tif,GFAP,Processes,Yes,Yes,,,,2000,4000,15000,13000
S1_R3C4.tif,Doublecortin,"Soma, Processes",Yes,Yes,S1_R2C4.tif,,,2000,4000,15000,13000
S1_R3C5.tif,S100,"Soma, Processes",Yes,Yes,S1_R3C3.tif,S1_R3C7.tif,,2000,4000,15000,13000
S1_R3C6.tif,Nestin,Processes,Yes,Yes,S1_R3C5.tif,S1_R2C4.tif,,2000,4000,15000,13000
S1_R3C7.tif,Aquaporin-4,Plasma Membrane,Yes,Yes,S1_R3C9.tif,S1_R3C5.tif,S1_R3C8.tif,2000,4000,15000,13000
S1_R3C8.tif,Tomato Lectin,Plasma Membrane,Yes,Yes,S1_R3C3.tif,,,2000,4000,15000,13000
S1_R3C9.tif,GLAST,Plasma Membrane,Yes,Yes,S1_R3C7.tif,,,2000,4000,15000,13000
S1_R4C1.tif,DAPI,Nucleus,Yes,Yes,,,,2000,4000,15000,13000
S1_R4C10.tif,Eomes,Nucleus,Yes,Yes,S1_R4C9.tif,S1_R4C8.tif,S1_R3C10.tif,2000,4000,15000,13000
S1_R4C11.tif,Phase Contrast Bright Field,Cell Morphology,No,No,,,,2000,4000,15000,13000
S1_R4C2.tif,Histones,Nucleus,Yes,Yes,,,,2000,4000,15000,13000
S1_R4C3.tif,Autofluorescence,N/A,Yes,Yes,,,,2000,4000,15000,13000
S1_R4C4.tif,PCNA,Nucleus,Yes,Yes,S1_R3C7.tif,,,2000,4000,15000,13000
S1_R4C5.tif,Sox2,Nucleus,Yes,Yes,S1_R4C7.tif,,,2000,4000,15000,13000
S1_R4C6.tif,GAD67,"Soma, Processes",Yes,Yes,S1_R4C5.tif,S1_R4C7.tif,,2000,4000,15000,13000
S1_R4C7.tif,Autofluorescence,N/A,Yes,Yes,,,,2000,4000,15000,13000
S1_R4C8.tif,Tomato Lectin,Plasma Membrane,Yes,Yes,,,,2000,4000,15000,13000
S1_R4C9.tif,Tbr1,Nucleus,Yes,Yes,,,,2000,4000,15000,13000
S1_R5C1.tif,DAPI,Nucleus,Yes,Yes,,,,2000,4000,15000,13000
S1_R5C10.tif,Calbindin,"Soma, Processes",Yes,Yes,S1_R5C9.tif,,,2000,4000,15000,13000
S1_R5C11.tif,Phase Contrast Bright Field,Cell Morphology,No,No,,,,2000,4000,15000,13000
S1_R5C2.tif,Histones,Nucleus,Yes,Yes,,,,2000,4000,15000,13000
S1_R5C3.tif,Calretinin,"Soma, Processes",Yes,Yes,S1_R2C3.tif,,,2000,4000,15000,13000
S1_R5C4.tif,CNPase,"Soma, Processes",Yes,Yes,S1_R2C4.tif,,,2000,4000,15000,13000
S1_R5C5.tif,Neurofilament-H,Processes,Yes,No,,,,2000,4000,15000,13000
S1_R5C6.tif,Myelin Basic Protein,Processes,Yes,No,,,,2000,4000,15000,13000
S1_R5C7.tif,Neurofilament-M,Processes,Yes,No,,,,2000,4000,15000,13000
S1_R5C8.tif,Tomato Lectin,Plasma Membrane,Yes,Yes,S1_R5C4.tif,,,2000,4000,15000,13000
S1_R5C9.tif,MAP2,"Soma, Processes",Yes,No,,,,2000,4000,15000,13000
R1C1.tif,DAPI,Nucleus,Yes,Yes,,,,2000,4000,15000,13000
R1C10.tif,Cleaved Caspase-3,Cytoplasm,Yes,Yes,R1C7.tif,R1C4.tif,R1C6.tif,2000,4000,15000,13000
R1C11.tif,Phase Contrast Bright Field,Cell Morphology,No,No,,,,2000,4000,15000,13000
R1C2.tif,Tyrosine Hydroxylase (TH),"Soma, Processes",Yes,Yes,R1C1.tif,,,19000,18500,21000,19500
R1C3.tif,Blood Brain Barrier,Plasma Membrane,Yes,Yes,,,,2000,4000,15000,13000
R1C4.tif,GFP,Cytoplasm,Yes,Yes,,,,2000,4000,15000,13000
R1C5.tif,Iba1,"Soma, Processes",Yes,Yes,,,,2000,4000,15000,13000
R1C6.tif,RECA1,Plasma Membrane,Yes,Yes,,,,2000,4000,15000,13000
R1C7.tif,Aquaporin-4,Plasma Membrane,Yes,Yes,R1C4.tif,,,2000,4000,15000,13000
R1C8.tif,Tomato Lectin,Plasma Membrane,Yes,Yes,,,,2000,4000,15000,13000
R1C9.tif,Olig2,Nucleus,Yes,Yes,R1C7.tif,R1C4.tif,R2C4.tif,2000,4000,15000,13000
R2C1.tif,DAPI,Nucleus,Yes,Yes,,,,2000,4000,15000,13000
R2C10.tif,Smooth Muscle Actin,"Soma, Processes",Yes,Yes,,,,2000,4000,15000,13000
R2C11.tif,Phase Contrast Bright Field,Cell Morphology,No,No,,,,2000,4000,15000,13000
R2C2.tif,Histones,Nucleus,Yes,Yes,,,,2000,4000,15000,13000
R2C3.tif,PDGFR beta,Plasma Membrane,Yes,Yes,R2C6.tif,,,2000,4000,15000,13000
R2C4.tif,NeuN,Nucleus,Yes,Yes,,,,2000,4000,15000,13000
R2C5.tif,Synaptohysin,Synapses,Yes,Yes,R2C6.tif,,,2000,4000,15000,13000
R2C6.tif,Parvalbumin,"Soma, Processes",Yes,Yes,,,,2000,4000,15000,13000
R2C7.tif,Choline Acetyltransferase,"Soma, Processes",Yes,Yes,R2C9.tif,R2C4.tif,R2C5.tif,28000,15400,36600,21200
R2C8.tif,Tomato Lectin,Plasma Membrane,Yes,Yes,,,,2000,4000,15000,13000
R2C9.tif,Glutaminase,"Soma, Processes",Yes,Yes,R2C7.tif,,,2000,4000,15000,13000
R3C1.tif,DAPI,Nucleus,Yes,Yes,,,,2000,4000,15000,13000
R3C10.tif,Vimentin,Processes,Yes,Yes,,,,2000,4000,15000,13000
R3C11.tif,Phase Contrast Bright Field,Cell Morphology,No,No,,,,2000,4000,15000,13000
R3C2.tif,Histones,Nucleus,Yes,Yes,,,,2000,4000,15000,13000
R3C3.tif,GFAP,Processes,Yes,Yes,,,,2000,4000,15000,13000
R3C4.tif,Doublecortin,"Soma, Processes",Yes,Yes,R2C4.tif,,,2000,4000,15000,13000
R3C5.tif,S100,"Soma, Processes",Yes,Yes,R3C3.tif,R3C7.tif,,2000,4000,15000,13000
R3C6.tif,Nestin,Processes,Yes,Yes,R3C5.tif,R2C4.tif,,2000,4000,15000,13000
R3C7.tif,Aquaporin-4,Plasma Membrane,Yes,Yes,R3C9.tif,R3C5.tif,R3C8.tif,2000,4000,15000,13000
R3C8.tif,Tomato Lectin,Plasma Membrane,Yes,Yes,R3C3.tif,,,2000,4000,15000,13000
R3C9.tif,GLAST,Plasma Membrane,Yes,Yes,R3C7.tif,,,2000,4000,15000,13000
R4C1.tif,DAPI,Nucleus,Yes,Yes,,,,2000,4000,15000,13000
R4C10.tif,Eomes,Nucleus,Yes,Yes,R4C9.tif,R4C8.tif,R3C10.tif,2000,4000,15000,13000
R4C11.tif,Phase Contrast Bright Field,Cell Morphology,No,No,,,,2000,4000,15000,13000
R4C2.tif,Histones,Nucleus,Yes,Yes,,,,2000,4000,15000,13000
R4C3.tif,Autofluorescence,N/A,Yes,Yes,,,,2000,4000,15000,13000
R4C4.tif,PCNA,Nucleus,Yes,Yes,R3C7.tif,,,2000,4000,15000,13000
R4C5.tif,Sox2,Nucleus,Yes,Yes,R4C7.tif,,,2000,4000,15000,13000
R4C6.tif,GAD67,"Soma, Processes",Yes,Yes,R4C5.tif,R4C7.tif,,2000,4000,15000,13000
R4C7.tif,Autofluorescence,N/A,Yes,Yes,,,,2000,4000,15000,13000
R4C8.tif,Tomato Lectin,Plasma Membrane,Yes,Yes,,,,2000,4000,15000,13000
R4C9.tif,Tbr1,Nucleus,Yes,Yes,,,,2000,4000,15000,13000
R5C1.tif,DAPI,Nucleus,Yes,Yes,,,,2000,4000,15000,13000
R5C10.tif,Calbindin,"Soma, Processes",Yes,Yes,R5C9.tif,,,2000,4000,15000,13000
R5C11.tif,Phase Contrast Bright Field,Cell Morphology,No,No,,,,2000,4000,15000,13000
R5C2.tif,Histones,Nucleus,Yes,Yes,,,,2000,4000,15000,13000
R5C3.tif,Calretinin,"Soma, Processes",Yes,Yes,R2C3.tif,,,2000,4000,15000,13000
R5C4.tif,CNPase,"Soma, Processes",Yes,Yes,R2C4.tif,,,2000,4000,15000,13000
R5C5.tif,Neurofilament-H,Processes,Yes,No,,,,2000,4000,15000,13000
R5C6.tif,Myelin Basic Protein,Processes,Yes,No,,,,2000,4000,15000,13000
R5C7.tif,Neurofilament-M,Processes,Yes,No,,,,2000,4000,15000,13000
R5C8.tif,Tomato Lectin,Plasma Membrane,Yes,Yes,R5C4.tif,,,2000,4000,15000,13000
R5C9.tif,MAP2,"Soma, Processes",Yes,No,,,,2000,4000,15000,13000
2 changes: 1 addition & 1 deletion scripts/slurm/biowulf/job_reconstruction.sh
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source deactivate
conda activate /data/jahanipourj2/software/miniconda/envs/brain

python /data/jahanipourj2/codes/whole_brain_analysis/main_reconstruction_lin.py \
python /data/jahanipourj2/codes/whole_brain_analysis/main_reconstruction.py \
--INPUT_DIR=/data/jahanipourj2/datasets/50PLX/S3/original \
--OUTPUT_DIR=/data/jahanipourj2/datasets/50PLX/S3 \
--MODE=supervised \
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2 changes: 1 addition & 1 deletion scripts/slurm/maui/maui_reconstruction.sh
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Expand Up @@ -9,7 +9,7 @@
source /project/ece/roysam/jahandar/software/miniconda/bin/activate /project/ece/roysam/jahandar/software/miniconda/envs/brain


python main_reconstruction_lin.py \
python main_reconstruction.py \
--INPUT_DIR=/project/hnguyen/datasets/TBI/G3_mFPI_Vehicle/G3_BR#18_HC_14L/original \
--OUTPUT_DIR=/project/hnguyen/datasets/TBI/G3_mFPI_Vehicle/G3_BR#18_HC_14L \
--MODE=supervised \
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2 changes: 1 addition & 1 deletion scripts/slurm/sabine/sabine_reconstrution.sh
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Expand Up @@ -10,7 +10,7 @@
module load Anaconda3
source activate /brazos/roysam/shared/miniconda/envs/brain

python main_reconstruction_lin.py \
python main_reconstruction.py \
--INPUT_DIR=/brazos/roysam/datasets/TBI/G2_Sham_Trained/G2_BR#22_HC_13L/original \
--OUTPUT_DIR=/brazos/roysam/datasets/TBI/G2_Sham_Trained/G2_BR#22_HC_13L \
--MODE=supervised \
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0 setup_env_lin.py → setup_env.py
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