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SarahMuthSarahMuth
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make training more usable
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‎models_az_thin/split-chemical_fixation.json‎

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{"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

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{"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

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{"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

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{"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

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{"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

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{"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

Lines changed: 3 additions & 2 deletions
Original file line numberDiff line numberDiff line change
@@ -2,12 +2,13 @@
22
#SBATCH -c 4 #4 #8
33
#SBATCH --mem 256G #120G #32G #64G #256G
44
#SBATCH -p grete:shared #grete:shared #grete-h100:shared
5-
#SBATCH -t 48:00:00 #6:00:00 #48:00:00
5+
#SBATCH -t 12:00:00 #6:00:00 #48:00:00
66
#SBATCH -G A100:1 #V100:1 #2 #A100:1 #gtx1080:2 #v100:1 #H100:1
77
#SBATCH --output=/user/muth9/u12095/synapse-net/slurm_revision/slurm-%j.out
88
#SBATCH -A nim00007
99
#SBATCH --constraint 80gb
1010

1111
source ~/.bashrc
1212
conda activate synapse-net
13-
python /user/muth9/u12095/synapse-net/scripts/cooper/revision/train_az.py -k az_merged_v6
13+
python /user/muth9/u12095/synapse-net/scripts/cooper/revision/az_prediction.py -v 7 --names 20241019_Tomo-eval_MF_Synapse 20241019_Tomo-eval_PS_Synapse \
14+
-i /mnt/lustre-emmy-hdd/projects/nim00007/data/synaptic-reconstruction/cooper/ground_truth/04Dataset_for_vesicle_eval

‎scripts/cooper/revision/az_prediction.py‎

Lines changed: 25 additions & 6 deletions
Original file line numberDiff line numberDiff line change
@@ -1,5 +1,6 @@
11
import argparse
22
import os
3+
from glob import glob
34

45
import h5py
56
from synapse_net.inference.active_zone import segment_active_zone
@@ -9,22 +10,28 @@
910
from common import get_file_names, get_split_folder, ALL_NAMES, INPUT_ROOT, OUTPUT_ROOT
1011

1112

12-
def run_prediction(model, name, split_folder, version, split_names):
13-
file_names = get_file_names(name, split_folder, split_names=split_names)
13+
def run_prediction(model, name, split_folder, version, split_names, input_path):
14+
if input_path:
15+
file_names =glob(os.path.join(input_path, name, "*.h5"))
16+
else:
17+
file_names = get_file_names(name, split_folder, split_names=split_names)
1418

1519
output_folder = os.path.join(OUTPUT_ROOT, name)
1620
os.makedirs(output_folder, exist_ok=True)
1721
output_key = f"predictions/az/v{version}"
1822

1923
for fname in tqdm(file_names):
24+
input_path = os.path.join(INPUT_ROOT, name, fname)
25+
print(f"segmenting {input_path}")
26+
2027
output_path = os.path.join(output_folder, fname)
2128

2229
if os.path.exists(output_path):
2330
with h5py.File(output_path, "r") as f:
2431
if output_key in f:
32+
print(f"skipping, because {output_key} already exists in {output_path}")
2533
continue
2634

27-
input_path = os.path.join(INPUT_ROOT, name, fname)
2835
with h5py.File(input_path, "r") as f:
2936
raw = f["raw"][:]
3037

@@ -34,10 +41,12 @@ def run_prediction(model, name, split_folder, version, split_names):
3441

3542

3643
def get_model(version):
37-
assert version in (3, 4, 5)
44+
assert version in (3, 4, 5, 7)
3845
split_folder = get_split_folder(version)
3946
if version == 3:
4047
model_path = os.path.join(split_folder, "checkpoints", "3D-AZ-model-TEM_STEM_ChemFix_wichmann-v3")
48+
elif version == 7:
49+
model_path = "/mnt/lustre-emmy-hdd/usr/u12095/synapse_net/models/ConstantinAZ/checkpoints/v7/"
4150
else:
4251
model_path = os.path.join(split_folder, "checkpoints", f"v{version}")
4352
model = load_model(model_path)
@@ -49,12 +58,22 @@ def main():
4958
parser.add_argument("--version", "-v", type=int)
5059
parser.add_argument("--names", nargs="+", default=ALL_NAMES)
5160
parser.add_argument("--splits", nargs="+", default=["test"])
61+
parser.add_argument("--model_path", default=None)
62+
parser.add_argument("--input", "-i", default=None)
63+
5264
args = parser.parse_args()
5365

54-
model = get_model(args.version)
66+
if args.model_path:
67+
model = load_model(model_path)
68+
else:
69+
model = get_model(args.version)
70+
5571
split_folder = get_split_folder(args.version)
72+
5673
for name in args.names:
57-
run_prediction(model, name, split_folder, args.version, args.splits)
74+
run_prediction(model, name, split_folder, args.version, args.splits, args.input)
75+
76+
print("Finished segmenting!")
5877

5978

6079
if __name__ == "__main__":

‎scripts/cooper/revision/common.py‎

Lines changed: 3 additions & 3 deletions
Original file line numberDiff line numberDiff line change
@@ -5,13 +5,13 @@
55
# The root folder which contains the new AZ training data.
66
INPUT_ROOT = "/mnt/ceph-hdd/cold/nim00007/new_AZ_train_data"
77
# The output folder for AZ predictions.
8-
OUTPUT_ROOT = "/mnt/ceph-hdd/cold/nim00007/AZ_prediction_new_copy"
8+
OUTPUT_ROOT = "/mnt/ceph-hdd/cold/nim00007/AZ_prediction_new"
99

1010
# The names of all datasets for which to run prediction / evaluation.
1111
# This excludes 'endbulb_of_held_cropped', which is a duplicate of 'endbulb_of_held',
1212
# which we don't evaluate on because of this.
1313
ALL_NAMES = [
14-
"chemical_fixation", "endbulb_of_held", "stem", "stem_cropped", "tem"
14+
"chemical_fixation", "endbulb_of_held", "stem", "tem"
1515
]
1616

1717
# The translation of new dataset names to old dataset names.
@@ -61,7 +61,7 @@ def get_file_names(name, split_folder, split_names):
6161

6262

6363
def get_split_folder(version):
64-
assert version in (3, 4, 5, 6)
64+
assert version in (3, 4, 5, 6, 7)
6565
if version == 3:
6666
split_folder = "splits"
6767
elif version == 6:

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