Revision Experiments

.gitignore

@@ -7,9 +7,16 @@ models/*/
 *.egg-info/
 run_sbatch.sbatch
 slurm/
+slurm_revision/
 scripts/cooper/evaluation_results/
 scripts/cooper/training/copy_testset.py
 scripts/rizzoli/upsample_data.py
 scripts/cooper/training/find_rec_testset.py
 synapse-net-models/
 scripts/portal/upscale_tomo.py
+analysis_results/
+scripts/cooper/revision/evaluation_results/
+scripts/cooper/revision/export_tif_to_h5.py
+scripts/cooper/revision/copy_path.py
+scripts/cooper/revision/view.py
+scripts/cooper/revision/count_AZ.py

environment.yaml

@@ -1,7 +1,7 @@
 channels:
     - conda-forge
 name:
-    synapse-net
+    synapse-net-cpu
 dependencies:
     - bioimageio.core
     - kornia

models_az_thin/split-chemical_fixation.json

@@ -0,0 +1 @@
+{"train": ["20180305_06_MS.h5", "20171113_01_MS.h5", "20171113_05_MS.h5", "20171113_04_MS.h5", "20180305_05_MS.h5", "20171113_3.2_MS.h5", "20180305_09_MS.h5", "20180305_07_MS.h5", "20180305_04_MS.h5", "20171006_2_2_MS.h5", "20171006_05_MS.h5", "20180305_10_MS.h5", "20171006_03_MS.h5", "20171006_2_3_MS.h5"], "val": ["20171013_01_MS.h5", "20171013_1.2_MS.h5", "20171006_3_2_MS.h5", "20180305_08_MS.h5", "20180305_02_MS.h5"], "test": ["20180305_03_MS.h5", "20171113_06_MS.h5", "20171113_07_MS.h5", "20171113_02_MS.h5", "20180305_01_MS.h5"]}

models_az_thin/split-endbulb_of_held.json

@@ -0,0 +1 @@
+{"train": ["M2_eb7_model.h5", "Wt22_eb1_10K_model2.h5", "WT40_eb5_model.h5", "KO8_eb4_model.h5", "M3_eb4_model.h5", "WT20_eb11_model2.h5", "WT13_syn6_model2.h5", "WT20_eb7_AZ1_model2.h5", "M2_eb10_model.h5", "WT11_syn1_model2.h5", "M8_eb8_model.h5", "WT22_eb10_model2.h5", "WT13_eb3_model2.h5", "WT20_syn7_model2.h5", "M7_eb6_model.h5", "WT20_eb7_AZ2_model2.h5", "WT13_syn5_model2.h5", "WT13_syn9_model2.h5", "M2_eb3_model.h5", "WT20_syn3_model2.h5", "WT20_syn1_model2.h5", "WT21_syn4_model2.h5", "WT20_eb4_model2.h5", "M2_eb9_model.h5", "M7_eb3_model.h5", "WT21_eb5_model2.h5", "WT22_eb6_AZ1_model2.h5", "WT13_syn10_model2.h5", "WT19_syn6_model2.h5", "M2_eb2_AZ2_model.h5", "WT41_eb4_model.h5", "WT13_syn4_model2.h5", "WT40_eb10_model.h5", "M1_eb8_model.h5", "WT19_syn9_model2.h5", "WT22_eb5_model2.h5", "WT39_eb7_model.h5", "KO9_eb13_model.h5", "WT39_eb5_model.h5", "WT11_eb5_model2.h5", "M7_eb15_model.h5", "M7_eb2_model.h5", "M7_eb9_model.h5", "WT22_syn7_model2.h5", "M1_eb7_model.h5", "WT11_syn6_model2.h5", "M7_eb5_model.h5", "WT22_syn5_model2.h5", "WT21_eb3_model2.h5", "WT19_syn3_model2.h5", "WT22_syn9_model2.h5", "M5_eb3_model.h5", "WT22_syn6_model2.h5", "WT39_eb9_model.h5", "WT13_eb5_model2.h5", "WT20_eb9_model2.h5", "WT20_eb2_AZ2_12K_model2.h5", "M7_eb12_model.h5", "M1_eb1_model.h5", "WT40_eb1_model.h5", "M2_eb6_model.h5", "M8_eb14_model.h5", "KO9_eb1_model.h5", "WT20_eb1_AZ2_12K_model2.h5", "M7_eb7_model.h5", "M8_eb9_model.h5", "WT40_eb11_model.h5", "M1_eb3_model.h5", "M8_eb12_model.h5", "M7_eb11_model.h5", "KO9_eb10_model.h5", "KO9_eb4_model.h5", "KO8_eb2_model.h5", "WT39_eb4_model.h5", "M1_eb5_model.h5", "M10_eb9_model.h5"], "val": ["WT41_eb6_model.h5", "Wt22_syn2_10K_model2.h5", "M1_eb6_model.h5", "KO9_eb11_model.h5", "WT20_eb5_model2.h5", "WT16_syn2_model2.h5", "KO9_eb9_model.h5", "WT21_eb7_model2.h5", "M7_eb4_model.h5", "M1_eb9_model.h5", "WT40_eb8_model.h5", "M2_eb5_model.h5", "WT13_eb4_model2.h5", "WT39_eb10_model.h5", "WT39_eb8_model.h5", "WT20_syn6_model2.h5", "WT13_syn11_model2.h5", "WT41_eb2_model.h5", "WT39_eb2_model.h5", "M2_eb14_model.h5", "M2_eb8_model.h5", "WT20_syn5_model2.h5", "M10_eb12_model.h5", "M5_eb1_model.h5", "KO9_eb12_model.h5"], "test": ["WT11_eb2_model2.h5", "WT21_syn5_model2.h5", "WT20_eb8_AZ2_model2.h5", "M10_eb8_model.h5", "WT21_eb9_model2.h5", "M2_eb1_model.h5", "WT22_syn10_model2.h5", "WT11_syn3_model2.h5", "WT11_eb1_model2.h5", "WT13_syn7_model2.h5", "WT21_eb4_model2.h5", "WT40_eb9_model.h5", "M6_eb2_model.h5", "WT22_syn1_10K_model2.h5", "WT19_syn1_model2.h5", "M7_eb10_model.h5", "KO9_eb6_model.h5", "WT11_eb7_model2.h5", "WT40_eb3_model.h5", "KO9_eb14_model.h5", "WT20_syn2_model2.h5", "WT22_eb9_model2.h5", "WT13_syn1_model2.h5", "WT39_eb3_model.h5", "WT21_syn3_model2.h5", "M8_eb6_model.h5"]}

models_az_thin/split-endbulb_of_held_cropped.json

@@ -0,0 +1 @@
+{"train": ["Wt22_eb1_10K_model2_cropped.h5", "WT22_eb6_AZ1_model2_cropped.h5", "WT21_eb3_model2_cropped.h5", "M7_eb11_model_cropped.h5", "WT20_syn3_model2_cropped.h5", "WT13_syn7_model2_cropped.h5", "WT13_eb4_model2_cropped.h5", "WT39_eb2_model_cropped.h5", "WT20_syn1_model2_cropped.h5", "WT40_eb3_model_cropped.h5", "WT20_eb7_AZ1_model2_cropped.h5", "WT21_syn5_model2_cropped.h5", "WT13_syn4_model2_cropped.h5", "KO9_eb13_model_cropped.h5", "M10_eb9_model_cropped.h5", "WT20_syn5_model2_cropped.h5", "M10_eb8_model_cropped.h5", "M7_eb12_model_cropped.h5", "WT39_eb7_model_cropped.h5", "WT20_eb4_model2_cropped.h5", "M1_eb8_model_cropped.h5", "WT40_eb11_model_cropped.h5", "KO9_eb14_model_cropped.h5", "WT39_eb10_model_cropped.h5", "KO9_eb6_model_cropped.h5", "WT13_syn1_model2_cropped.h5", "WT13_syn9_model2_cropped.h5", "WT13_eb3_model2_cropped.h5", "WT41_eb4_model_cropped.h5", "WT40_eb5_model_cropped.h5", "WT11_eb5_model2_cropped.h5", "WT22_eb9_model2_cropped.h5", "M2_eb2_AZ2_model_cropped.h5", "WT41_eb6_model_cropped.h5", "WT13_eb5_model2_cropped.h5", "WT13_syn11_model2_cropped.h5", "WT22_syn5_model2_cropped.h5", "WT20_syn6_model2_cropped.h5", "WT22_syn9_model2_cropped.h5", "WT11_syn6_model2_cropped.h5", "M8_eb12_model_cropped.h5", "WT39_eb4_model_cropped.h5", "M8_eb8_model_cropped.h5", "WT21_eb9_model2_cropped.h5", "WT39_eb3_model_cropped.h5", "M2_eb1_model_cropped.h5", "M2_eb9_model_cropped.h5", "WT39_eb5_model_cropped.h5", "WT22_eb10_model2_cropped.h5", "M7_eb4_model_cropped.h5", "WT20_eb7_AZ2_model2_cropped.h5", "WT40_eb10_model_cropped.h5", "WT19_syn9_model2_cropped.h5", "WT22_syn6_model2_cropped.h5", "WT11_eb1_model2_cropped.h5", "M10_eb12_model_cropped.h5", "KO9_eb11_model_cropped.h5", "WT19_syn6_model2_cropped.h5", "M7_eb5_model_cropped.h5", "WT39_eb9_model_cropped.h5", "M2_eb14_model_cropped.h5", "Wt22_syn2_10K_model2_cropped.h5", "WT20_syn2_model2_cropped.h5", "M7_eb9_model_cropped.h5", "M5_eb3_model_cropped.h5", "WT22_syn1_10K_model2_cropped.h5", "M1_eb7_model_cropped.h5", "M1_eb6_model_cropped.h5", "M7_eb7_model_cropped.h5", "WT21_eb7_model2_cropped.h5", "M2_eb8_model_cropped.h5", "WT20_eb1_AZ2_12K_model2_cropped.h5", "WT20_eb9_model2_cropped.h5", "WT41_eb2_model_cropped.h5", "WT20_eb5_model2_cropped.h5", "KO9_eb12_model_cropped.h5", "M3_eb4_model_cropped.h5", "WT19_syn1_model2_cropped.h5", "M2_eb3_model_cropped.h5", "KO9_eb9_model_cropped.h5", "WT13_syn5_model2_cropped.h5", "M1_eb1_model_cropped.h5", "M2_eb5_model_cropped.h5", "WT20_eb11_model2_cropped.h5", "WT13_syn6_model2_cropped.h5", "KO9_eb10_model_cropped.h5", "M2_eb7_model_cropped.h5", "M1_eb5_model_cropped.h5", "WT13_syn10_model2_cropped.h5", "WT22_eb5_model2_cropped.h5", "KO8_eb2_model_cropped.h5", "M2_eb10_model_cropped.h5", "KO9_eb1_model_cropped.h5", "M7_eb10_model_cropped.h5", "WT21_syn3_model2_cropped.h5", "WT40_eb8_model_cropped.h5"], "val": ["WT20_eb2_AZ2_12K_model2_cropped.h5", "WT19_syn3_model2_cropped.h5", "M6_eb2_model_cropped.h5", "M8_eb9_model_cropped.h5", "KO8_eb4_model_cropped.h5", "WT21_eb4_model2_cropped.h5", "WT22_syn10_model2_cropped.h5", "WT20_syn7_model2_cropped.h5", "M7_eb3_model_cropped.h5", "M7_eb6_model_cropped.h5", "WT16_syn2_model2_cropped.h5", "WT39_eb8_model_cropped.h5", "KO9_eb4_model_cropped.h5", "M1_eb9_model_cropped.h5", "M2_eb6_model_cropped.h5", "WT11_syn1_model2_cropped.h5", "WT11_eb7_model2_cropped.h5", "M1_eb3_model_cropped.h5", "WT21_eb5_model2_cropped.h5", "WT11_syn3_model2_cropped.h5", "M8_eb6_model_cropped.h5", "WT21_syn4_model2_cropped.h5", "M7_eb15_model_cropped.h5", "WT22_syn7_model2_cropped.h5"]}

models_az_thin/split-stem.json

@@ -0,0 +1 @@
+{"train": ["36859_H3_SP_10_rec_2kb1dawbp_crop.h5", "36859_H3_SP_01_rec_2kb1dawbp_crop.h5", "36859_H2_SP_02_rec_2Kb1dawbp_crop.h5", "36859_H2_SP_03_rec_2Kb1dawbp_crop.h5"], "val": ["36859_H3_SP_05_rec_2kb1dawbp_crop.h5", "36859_H2_SP_01_rec_2Kb1dawbp_crop.h5"], "test": ["36859_H3_SP_07_rec_2kb1dawbp_crop.h5", "36859_J1_STEM750_66K_SP_03_rec_2kb1dawbp_crop.h5"]}

models_az_thin/split-stem_cropped.json

@@ -0,0 +1 @@
+{"train": ["36859_J1_66K_TS_CA3_PS_23_rec_2Kb1dawbp_crop_crop1.h5", "36859_J1_STEM750_66K_SP_15_rec_2kb1dawbp_crop_crop1.h5", "36859_J1_66K_TS_CA3_PS_43_rec_2Kb1dawbp_crop_crop1.h5", "36859_H2_SP_01_rec_2Kb1dawbp_crop_crop1.h5", "36859_J1_STEM750_66K_SP_10_rec_2kb1dawbp_crop_crop1.h5", "36859_H3_SP_05_rec_2kb1dawbp_crop_crop1.h5", "36859_J1_STEM750_66K_SP_07_rec_2kb1dawbp_crop_crop2.h5", "36859_H2_SP_01_rec_2Kb1dawbp_crop_crop2.h5", "36859_J1_STEM750_66K_SP_08_rec_2kb1dawbp_crop_crop3.h5", "36859_H3_SP_07_rec_2kb1dawbp_crop_crop2.h5", "36859_H3_SP_07_rec_2kb1dawbp_crop_cropped_noAZ.h5", "36859_J1_STEM750_66K_SP_03_rec_2kb1dawbp_crop_crop1.h5", "36859_J1_STEM750_66K_SP_06_rec_2kb1dawbp_crop_crop1.h5", "36859_H2_SP_03_rec_2Kb1dawbp_crop_crop1.h5", "36859_H3_SP_07_rec_2kb1dawbp_crop_crop1.h5", "36859_J1_STEM750_66K_SP_02_rec_2kb1dawbp_crop_crop1.h5", "36859_J1_STEM750_66K_SP_17_rec_2kb1dawbp_crop_crop1.h5", "36859_H2_SP_11_rec_2Kb1dawbp_crop_crop1.h5", "36859_H2_SP_04_rec_2Kb1dawbp_crop_crop1.h5", "36859_H2_SP_04_rec_2Kb1dawbp_crop_crop2.h5", "36859_H3_SP_10_rec_2kb1dawbp_crop_cropped_noAZ.h5", "36859_H2_SP_06_rec_2Kb1dawbp_crop_crop1.h5", "36859_J1_66K_TS_CA3_PS_26_rec_2Kb1dawbp_crop_crop1.h5", "36859_J1_STEM750_66K_SP_14_rec_2kb1dawbp_crop_crop2.h5", "36859_H3_SP_01_rec_2kb1dawbp_crop_crop1.h5", "36859_H2_SP_01_rec_2Kb1dawbp_crop_crop3.h5", "36859_J1_STEM750_66K_SP_13_rec_2kb1dawbp_crop_crop2.h5", "36859_H2_SP_10_rec_crop_crop1.h5", "36859_H2_SP_02_rec_2Kb1dawbp_crop_cropped_noAZ.h5", "36859_J1_66K_TS_CA3_PS_32_rec_2Kb1dawbp_crop_crop1.h5", "36859_J1_STEM750_66K_SP_01_rec_2kb1dawbp_crop_crop1.h5", "36859_H2_SP_03_rec_2Kb1dawbp_crop_cropped_noAZ.h5", "36859_H3_SP_10_rec_2kb1dawbp_crop_crop1.h5", "36859_H2_SP_02_rec_2Kb1dawbp_crop_crop1.h5", "36859_J1_STEM750_66K_SP_08_rec_2kb1dawbp_crop_crop2.h5", "36859_J1_STEM750_66K_SP_03_rec_2kb1dawbp_crop_crop2.h5", "36859_H3_SP_05_rec_2kb1dawbp_crop_crop2.h5", "36859_H2_SP_07_rec_2Kb1dawbp_crop_crop1.h5", "36859_J1_STEM750_66K_SP_13_rec_2kb1dawbp_crop_crop1.h5", "36859_J1_STEM750_66K_SP_14_rec_2kb1dawbp_crop_crop1.h5"], "val": ["36859_J1_STEM750_66K_SP_03_rec_2kb1dawbp_crop_crop3.h5", "36859_H2_SP_01_rec_2Kb1dawbp_crop_cropped_noAZ.h5", "36859_J1_STEM750_66K_SP_08_rec_2kb1dawbp_crop_crop1.h5", "36859_J1_STEM750_66K_SP_12_rec_2kb1dawbp_crop_crop1.h5", "36859_H3_SP_05_rec_2kb1dawbp_crop_cropped_noAZ.h5", "36859_H3_SP_09_rec_2kb1dawbp_crop_crop1.h5", "36859_J1_STEM750_66K_SP_11_rec_2kb1dawbp_crop_crop1.h5", "36859_J1_STEM750_66K_SP_07_rec_2kb1dawbp_crop_crop1.h5", "36859_J1_STEM750_66K_SP_12_rec_2kb1dawbp_crop_crop2.h5", "36859_J1_STEM750_66K_SP_10_rec_2kb1dawbp_crop_crop2.h5"]}

models_az_thin/split-tem.json

@@ -0,0 +1 @@
+{"train": ["20190805_09002_B4_SC_08_SP.h5", "WT_MF_DIV28_3.2_MS_09204_K1.h5", "20190524_09204_F4_SC_09_SP.h5", "20190524_09204_F4_SC_06_SP.h5", "WT_MF_DIV14_6.2_MS_E2_09175_CA3_2.h5", "WT_MF_DIV14_07_MS_C2_09175_CA3.h5", "WT_Unt_SC_09175_C4_04_DIV15_mtk_04.h5", "M13_CTRL_22723_O3_06_DIV29_06_MS.h5", "WT_Unt_SC_09175_E2_04_DIV14_mtk_03.h5", "WT_MF_DIV14_01_MS_E2_09175_CA3.h5", "M13_CTRL_22723_J1_03_DIV29_03_MS.h5", "20190807_23032_D4_SC_03_SP.h5", "M13_DKO_09201_U1_05_DIV31_05_MS.h5", "WT_Unt_SC_09175_E4_02_DIV14_mtk_02.h5", "20190805_09002_B4_SC_01_SP.h5", "WT_Unt_SC_09175_C4_08_DIV15_mtk_08.h5", "WT_MF_DIV14_01_MS_B2_09175_CA3.h5", "20190805_09002_B4_SC_10_SP.h5", "WT_Unt_SC_09175_D4_01_DIV14_mtk_01.h5", "WT_Unt_SC_09175_E2_03_DIV14_mtk_03.h5", "WT_Unt_SC_09175_C4_02_DIV15_mtk_02.h5", "20190805_09002_B4_SC_12_SP.h5", "20190805_09002_B4_SC_02_SP.h5", "M13_DKO_09201_U1_04_DIV31_04_MS.h5", "WT_MF_DIV14_02_MS_D2_09175_CA3.h5", "WT_Unt_SC_09175_E2_05_DIV14_mtk_05.h5", "20190807_23032_D4_SC_07_SP.h5", "M13_CTRL_09201_S2_03_DIV31_03_MS.h5", "WT_MF_DIV14_01.2_MS_D1_09175_CA3.h5", "20190807_23032_D4_SC_01_SP.h5", "WT_Unt_SC_09175_E4_03_DIV14_mtk_03.h5", "WT_MF_DIV28_3.3_MS_09204_K1.h5", "WT_Unt_SC_09175_D5_04_DIV14_mtk_04.h5", "20190524_09204_F4_SC_05_SP.h5", "M13_DKO_22723_A1_03_DIV29_03_MS.h5", "20190805_09002_B4_SC_7.2_SP.h5", "M13_DKO_22723_A4_08_DIV29_08_MS.h5", "WT_Unt_SC_09175_E4_05_DIV14_mtk_05.h5", "M13_CTRL_09201_S1_01_DIV31_01.h5", "WT_Unt_SC_09175_C4_03_DIV15_mtk_03.h5", "WT_MF_DIV28_03_MS_09204_M1.h5", "M13_DKO_09201_U1_5.2_DIV31_5.2_MS.h5", "WT_Unt_SC_09175_E2_01_DIV14_mtk_01.h5", "WT_MF_DIV28_2.3_MS_09002_B1.h5", "WT_MF_DIV28_01_MS_09204_F1.h5", "M13_CTRL_09201_S2_05_DIV31_05_MS.h5", "20190807_23032_D4_SC_04_SP.h5", "M13_DKO_09201_Q1_04_DIV31_04_MS.h5", "WT_MF_DIV28_04_MS_09204_M1.h5", "WT_Unt_SC_09175_D4_04_DIV14_mtk_04.h5", "WT_MF_DIV14_02_MS_B2_09175_CA3.h5", "20190807_23032_D4_SC_10_SP.h5", "M13_DKO_09201_U1_03_DIV31_03_MS.h5", "WT_MF_DIV14_01_MS_D1_09175_CA3.h5", "WT_MF_DIV28_05_MS_09204_F1.h5", "WT_Unt_SC_09175_D4_05_DIV14_mtk_05.h5", "WT_MF_DIV14_01_MS_D2_09175_CA3.h5", "WT_MF_DIV28_03_MS_09204_K1.h5", "M13_DKO_09201_O1_01_DIV31_01_MS.h5", "WT_MF_DIV14_04_MS_C2_09175_CA3.h5", "20190524_09204_F4_SC_04_SP.h5", "WT_MF_DIV14_02_MS_E1_09175_CA3.h5", "20190807_23032_D4_SC_09_SP.h5", "M13_CTRL_22723_O2_04_DIV29_04_MS.h5", "WT_MF_DIV28_03_MS_09204_F1.h5", "WT_MF_DIV28_01_MS_09002_B1.h5", "20190524_09204_F4_SC_03_SP.h5", "M13_DKO_22723_A1_4.2_DIV29_4.2_MS.h5", "M13_DKO_23037_K1_01_DIV29_01_MS.h5", "M13_DKO_23037_K1_1.2_DIV29_1.2_MS.h5", "20190524_09204_F4_SC_11_SP.h5", "WT_MF_DIV28_1.2_MS_09204_F1.h5", "M13_DKO_09201_O3_06_DIV31_06_MS.h5", "WT_Unt_SC_09175_C4_01_DIV15_mtk_01.h5", "WT_MF_DIV14_3.2_MS_D2_09175_CA3.h5", "WT_MF_DIV28_07_MS_09002_B2.h5", "WT_MF_DIV28_06_MS_09204_F1.h5", "M13_CTRL_09201_S2_04_DIV31_04_MS.h5", "WT_MF_DIV28_1.2_MS_09002_B1.h5", "WT_MF_DIV28_3.4_MS_09204_K1.h5", "20190524_09204_F4_SC_10_SP.h5", "20190805_09002_B4_SC_11_SP.h5", "20190524_09204_F4_SC_01_SP.h5", "WT_Unt_SC_09175_C4_05_DIV15_mtk_05.h5", "WT_MF_DIV28_04_MS_09002_B2.h5"], "val": ["WT_MF_DIV28_02_MS_09002_B1.h5", "M13_CTRL_09201_S2_06_DIV31_06_MS.h5", "20190805_09002_B4_SC_05_SP.h5", "WT_MF_DIV14_04_MS_B2_09175_CA3.h5", "M13_CTRL_22723_O3_07_DIV29_07_MS.h5", "WT_MF_DIV14_03.2_MS_D1_09175_CA3.h5", "WT_MF_DIV14_04_MS_E1_09175_CA3.h5", "20190524_09204_F4_SC_07_SP.h5", "WT_MF_DIV28_08_MS_09204_F2.h5", "WT_MF_DIV14_06_MS_C2_09175_CA3.h5", "WT_Unt_SC_09175_B5_03_DIV16_mtk_05.h5", "WT_MF_DIV28_2.2_MS_09002_B1.h5", "WT_Unt_SC_09175_D4_02_DIV14_mtk_02.h5", "WT_MF_DIV28_04_MS_09204_F1.h5", "20190805_09002_B4_SC_04_SP.h5", "M13_DKO_09201_Q1_01_DIV31_01_MS.h5", "WT_MF_DIV28_02_MS_09204_M1.h5", "M13_CTRL_22723_O2_05_DIV29_05_MS_.h5", "20190807_23032_D4_SC_08_SP.h5", "WT_Unt_SC_09175_D5_05_DIV14_mtk_05.h5", "WT_Unt_SC_09175_D5_02_DIV14_mtk_02.h5", "WT_MF_DIV14_05_MS_B2_09175_CA3.h5", "WT_Unt_SC_09175_D5_01_DIV14_mtk_01.h5", "20190524_09204_F4_SC_02_SP.h5", "WT_Unt_SC_09175_E4_04_DIV14_mtk_04.h5", "M13_DKO_09201_O3_6.2_DIV31_6.2_MS.h5", "M13_DKO_22723_A1_05_DIV29_05_MS.h5", "WT_MF_DIV14_04_MS_E2_09175_CA3_2.h5", "WT_MF_DIV14_03_MS_C2_09175_CA3.h5"], "test": ["WT_MF_DIV28_4.2_MS_09204_M1.h5", "M13_DKO_09201_Q1_03_DIV31_03_MS.h5", "WT_MF_DIV14_3.1_MS_D2_09175_CA3.h5", "WT_Unt_SC_09175_B5_03_DIV16_mtk_04.h5", "WT_MF_DIV28_10_MS_09002_B3.h5", "WT_MF_DIV14_06_MS_E2_09175_CA3_2.h5", "WT_MF_DIV14_03.3_MS_D1_09175_CA3.h5", "20190805_09002_B4_SC_09_SP.h5", "20190805_09002_B4_SC_7.1_SP.h5", "WT_MF_DIV14_03.1_MS_D1_09175_CA3.h5", "WT_Unt_SC_09175_E4_01_DIV14_mtk_01.h5", "WT_MF_DIV28_09_MS_09002_B3.h5", "WT_Unt_SC_09175_B5_01_DIV16_mtk_01.h5", "M13_DKO_22723_A1_06_DIV29_06_MS.h5", "WT_MF_DIV14_01_MS_orig_C2_09175_CA3.h5", "20190807_23032_D4_SC_05_SP.h5", "M13_DKO_22723_A4_10_DIV29_10_MS.h5", "WT_MF_DIV14_05_MS_C2_09175_CA3.h5", "WT_MF_DIV28_07_MS_09204_F2.h5", "WT_Unt_SC_09175_D5_03_DIV14_mtk_03.h5", "M13_CTRL_22723_O2_05_DIV29_5.2.h5", "WT_MF_DIV14_02_MS_C2_09175_CA3.h5", "WT_Unt_SC_09175_B5_03_DIV16_mtk_03.h5", "WT_MF_DIV14_03_MS_B2_09175_CA3.h5", "WT_Unt_SC_09175_B5_02_DIV16_mtk_02.h5", "WT_Unt_SC_09175_C4_06_DIV15_mtk_06.h5", "WT_MF_DIV14_05_MS_E2_09175_CA3_2.h5", "M13_CTRL_09201_S2_02_DIV31_02_MS.h5", "WT_MF_DIV28_08_MS_09002_B3.h5"]}

run_sbatch_revision.sbatch

@@ -0,0 +1,16 @@
+#! /bin/bash
+#SBATCH -c 4 #4 #8
+#SBATCH --mem 256G #120G #32G #64G #256G
+#SBATCH -p grete:shared #grete:shared #grete-h100:shared
+#SBATCH -t 3:00:00 #6:00:00 #48:00:00 
+#SBATCH -G A100:1 #V100:1 #2 #A100:1  #gtx1080:2 #v100:1 #H100:1
+#SBATCH --output=/user/muth9/u12095/synapse-net/slurm_revision/slurm-%j.out 
+#SBATCH -A nim00007 
+#SBATCH --constraint 80gb 
+
+source ~/.bashrc
+conda activate synapse-net
+python /user/muth9/u12095/synapse-net/scripts/cooper/revision/updated_data_analysis/run_data_analysis.py \
+ -i /mnt/lustre-emmy-hdd/projects/nim00007/data/synaptic-reconstruction/cooper/20241102_TOMO_DATA_Imig2014/exported/SNAP25 \
+ -o /mnt/lustre-emmy-hdd/projects/nim00007/data/synaptic-reconstruction/cooper/20241102_TOMO_DATA_Imig2014/afterRevision_analysis/boundaryT0_9_constantins_presynapticFiltering/weaker_SVfilter/man_subset --store \
+ -s ./analysis_results/weaker_SVfilter/man_subset