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added results data and plotting nb for paper figures #40

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added results data and plotting nb for paper figures #40

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4dea00c
added results data and plotting nb for paper figures
ulisrael Feb 18, 2025
314f241
updated meta data naming for livecell
ulisrael Feb 18, 2025
862a633
rm old plotting script
ulisrael Feb 18, 2025
bff4d01
Modify paths in notebook.
rossbar Feb 18, 2025
5dcb955
Add more cruft to .gitignore.
rossbar Feb 18, 2025
00c2fec
Rm apple cruft.
rossbar Feb 18, 2025
475a4fa
updated pths so each section can be run independently
ulisrael Feb 18, 2025
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4 changes: 4 additions & 0 deletions 4 .gitignore
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Expand Up @@ -2,6 +2,7 @@
__pycache__/
build/
*.egg-info/
*.ipynb_checkpoints/

# Documentation cruft
docs/_build
Expand All @@ -10,3 +11,6 @@ docs/sg_execution_times.rst

# Editor cruft
*.swp

# Apple cruft
*.DS_Store
53 changes: 53 additions & 0 deletions 53 paper_figures/eval_results/all_results.txt
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cellsam_general,0.9305001530212429,deepbacs,dec_14_anchor_new_FT_classic_continuation_3_alt_new_sh_v3/checkpoint002739.pth
cellsam_general,0.9114955475266577,Gendarme_BriFi,dec_14_anchor_new_FT_classic_continuation_3_alt_new_sh_v3/checkpoint002739.pth
cellsam_general,0.9899636661100489,YeaZ,dec_14_anchor_new_FT_classic_continuation_3_alt_new_sh_v3/checkpoint002739.pth
cellsam_general,0.9947094282646641,YeastNet,dec_14_anchor_new_FT_classic_continuation_3_alt_new_sh_v3/checkpoint002739.pth
cellsam_general,0.8937110327485136,dsb_fixed,dec_14_anchor_new_FT_classic_continuation_3_alt_new_sh_v3/checkpoint002739.pth
cellsam_general,0.8664808313235363,cellpose,dec_14_anchor_new_FT_classic_continuation_3_alt_new_sh_v3/checkpoint002739.pth
cellsam_general,0.8247822940812387,H_and_E,dec_14_anchor_new_FT_classic_continuation_3_alt_new_sh_v3/checkpoint002739.pth
cellsam_general,0.9257042959658932,ep_phase_microscopy_all,dec_14_anchor_new_FT_classic_continuation_3_alt_new_sh_v3/checkpoint002739.pth
cellsam_general,0.8943925241426757,tissuenet_wholecell,dec_14_anchor_new_FT_classic_continuation_3_alt_new_sh_v3/checkpoint002739.pth
cellsam_general,0.846632516582404,omnipose,dec_14_anchor_new_FT_classic_continuation_3_alt_new_sh_v3/checkpoint002739.pth
cellpose_general,0.91238774051133,deepbacs,./training_january_2025/cellpose_20241009_cp3_epoch_500_LR_0.2_WD_1e-5_size/cellpose_mixed_Max_0_no_CLAHE_no_pad_0shot_chan_3_chan2_2.pt
cellpose_general,0.8669610653765454,Gendarme_BriFi,./training_january_2025/cellpose_20241009_cp3_epoch_500_LR_0.2_WD_1e-5_size/cellpose_mixed_Max_0_no_CLAHE_no_pad_0shot_chan_3_chan2_2.pt
cellpose_general,0.9899964366211056,YeaZ,./training_january_2025/cellpose_20241009_cp3_epoch_500_LR_0.2_WD_1e-5_size/cellpose_mixed_Max_0_no_CLAHE_no_pad_0shot_chan_3_chan2_2.pt
cellpose_general,0.9860846500005519,YeastNet,./training_january_2025/cellpose_20241009_cp3_epoch_500_LR_0.2_WD_1e-5_size/cellpose_mixed_Max_0_no_CLAHE_no_pad_0shot_chan_3_chan2_2.pt
cellpose_general,0.8856022519784442,dsb_fixed,./training_january_2025/cellpose_20241009_cp3_epoch_500_LR_0.2_WD_1e-5_size/cellpose_mixed_Max_0_no_CLAHE_no_pad_0shot_chan_3_chan2_2.pt
cellpose_general,0.814113454154465,cellpose,./training_january_2025/cellpose_20241009_cp3_epoch_500_LR_0.2_WD_1e-5_size/cellpose_mixed_Max_0_no_CLAHE_no_pad_0shot_chan_3_chan2_2.pt
cellpose_general,0.7748214122716256,H_and_E,./training_january_2025/cellpose_20241009_cp3_epoch_500_LR_0.2_WD_1e-5_size/cellpose_mixed_Max_0_no_CLAHE_no_pad_0shot_chan_3_chan2_2.pt
cellpose_general,0.936851178675501,ep_phase_microscopy_all,./training_january_2025/cellpose_20241009_cp3_epoch_500_LR_0.2_WD_1e-5_size/cellpose_mixed_Max_0_no_CLAHE_no_pad_0shot_chan_3_chan2_2.pt
cellpose_general,0.8646821528359615,tissuenet_wholecell,./training_january_2025/cellpose_20241009_cp3_epoch_500_LR_0.2_WD_1e-5_size/cellpose_mixed_Max_0_no_CLAHE_no_pad_0shot_chan_3_chan2_2.pt
cellpose_general,0.8384279997907049,omnipose,./training_january_2025/cellpose_20241009_cp3_epoch_500_LR_0.2_WD_1e-5_size/cellpose_mixed_Max_0_no_CLAHE_no_pad_0shot_chan_3_chan2_2.pt
cellpose_cyto3,0.9139431317609098,deepbacs,
cellpose_cyto3,0.050923936631913455,Gendarme_BriFi,
cellpose_cyto3,0.989047961509327,YeaZ,
cellpose_cyto3,0.660566884954237,YeastNet,
cellpose_cyto3,0.888261465326483,dsb_fixed,
cellpose_cyto3,0.8432707674791837,cellpose,
cellpose_cyto3,0.45903535855855365,H_and_E,
cellpose_cyto3,0.814325403862586,ep_phase_microscopy_all,
cellpose_cyto3,0.8769010241057854,tissuenet_wholecell,
cellpose_cyto3,0.8956352047235195,omnipose,
cellsam/individual,0.8921574794507869,deepbacs,./training_january_2025/anchor_01_25_cont_3/deepbacs/checkpoint002739.pth
cellsam/individual,0.8421975934312929,Gendarme_BriFi,./training_january_2025/anchor_01_25_cont_3/Gendarme_BriFi/checkpoint002739.pth
cellsam/individual,0.9909187269704174,YeaZ,./training_january_2025/anchor_01_25_cont_3/YeaZ/checkpoint002739.pth
cellsam/individual,0.9638221147978361,YeastNet,./training_january_2025/anchor_01_25_cont_3/YeastNet/checkpoint002739.pth
cellsam/individual,0.8917925414259174,dsb_fixed,./training_january_2025/anchor_01_25_cont_3/dsb_fixed/checkpoint002739.pth
cellsam/individual,0.8867571609282048,cellpose,./training_january_2025/anchor_01_25_cont_3/cellpose/checkpoint002739.pth
cellsam/individual,0.7436987996709924,H_and_E,./training_january_2025/anchor_01_25_cont_3/H_and_E/checkpoint002739.pth
cellsam/individual,0.9259990604360172,ep_phase_microscopy_all,./training_january_2025/anchor_01_25_cont_3/ep_phase_microscopy_all/checkpoint002739.pth
cellsam/individual,0.8938937567036123,tissuenet_wholecell,./training_january_2025/anchor_01_25_cont_3/tissuenet_wholecell/checkpoint002739.pth
cellsam/individual,0.8130231630030896,omnipose,./training_january_2025/anchor_01_25_cont_3/omnipose/checkpoint002739.pth
cellpose/individual,0.9267827061903309,deepbacs,./training_january_2025/cellpose_20241009_cp3_epoch_500_LR_0.2_WD_1e-5_size/cellpose_deepbacs_Max_0_no_CLAHE_no_pad_0shot_chan_3_chan2_2.pt
cellpose/individual,0.9250379189518813,Gendarme_BriFi,./training_january_2025/cellpose_20241009_cp3_epoch_500_LR_0.2_WD_1e-5_size/cellpose_Gendarme_BriFi_Max_0_no_CLAHE_no_pad_0shot_chan_3_chan2_2.pt
cellpose/individual,0.9904068807065127,YeaZ,./training_january_2025/cellpose_20241009_cp3_epoch_500_LR_0.2_WD_1e-5_size/cellpose_YeaZ_Max_0_no_CLAHE_no_pad_0shot_chan_3_chan2_2.pt
cellpose/individual,0.9972082561573762,YeastNet,./training_january_2025/cellpose_20241009_cp3_epoch_500_LR_0.2_WD_1e-5_size/cellpose_YeastNet_Max_0_no_CLAHE_no_pad_0shot_chan_3_chan2_2.pt
cellpose/individual,0.8879976689450022,dsb_fixed,./training_january_2025/cellpose_20241009_cp3_epoch_500_LR_0.2_WD_1e-5_size/cellpose_dsb_fixed_Max_0_no_CLAHE_no_pad_0shot_chan_3_chan2_2.pt
cellpose/individual,0.8559837120640661,cellpose,./training_january_2025/cellpose_20241009_cp3_epoch_500_LR_0.2_WD_1e-5_size/cellpose_cellpose_Max_0_no_CLAHE_no_pad_0shot_chan_3_chan2_2.pt
cellpose/individual,0.8108379796652139,H_and_E,./training_january_2025/cellpose_20241009_cp3_epoch_500_LR_0.2_WD_1e-5_size/cellpose_H_and_E_Max_0_no_CLAHE_no_pad_0shot_chan_3_chan2_2.pt
cellpose/individual,0.9384103928725154,ep_phase_microscopy_all,./training_january_2025/cellpose_20241009_cp3_epoch_500_LR_0.2_WD_1e-5_size/cellpose_ep_phase_microscopy_all_Max_0_no_CLAHE_no_pad_0shot_chan_3_chan2_2.pt
cellpose/individual,0.8719401414468197,tissuenet_wholecell,./training_january_2025/cellpose_20241009_cp3_epoch_500_LR_0.2_WD_1e-5_size/cellpose_tissuenet_wholecell_Max_0_no_CLAHE_no_pad_0shot_chan_3_chan2_2.pt
cellpose/individual,0.9078500423037477,omnipose,./training_january_2025/cellpose_20241009_cp3_epoch_500_LR_0.2_WD_1e-5_size/cellpose_omnipose_Max_0_no_CLAHE_no_pad_0shot_chan_3_chan2_2.pt
cellsam/general,0.3812593514569176,LIVECell_good,./training_january_2025/cellpose_20241009_cp3_epoch_500_LR_0.2_WD_1e-5_size/cellpose_mixed_Max_0_no_CLAHE_no_pad_0shot_chan_3_chan2_2.pt
cellpose/general,0.4993479290305242,LIVECell_good,dec_14_anchor_new_FT_classic_continuation_3_alt_new_sh_v3/checkpoint002739.pth
cellsam/general_FS_10_FT,0.6340405966856812,LIVECell_good,anchor_01_25_cont_fewshot/livecell/checkpoint002799.pth
22 changes: 22 additions & 0 deletions 22 paper_figures/eval_results/cellpose/cyto3/Gendarme_BriFi.txt
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51 changes: 51 additions & 0 deletions 51 paper_figures/eval_results/cellpose/cyto3/H_and_E.txt
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17 changes: 17 additions & 0 deletions 17 paper_figures/eval_results/cellpose/cyto3/YeaZ.txt
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15 changes: 15 additions & 0 deletions 15 paper_figures/eval_results/cellpose/cyto3/YeastNet.txt
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68 changes: 68 additions & 0 deletions 68 paper_figures/eval_results/cellpose/cyto3/cellpose.txt
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92 changes: 92 additions & 0 deletions 92 paper_figures/eval_results/cellpose/cyto3/deepbacs.txt
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56 changes: 56 additions & 0 deletions 56 paper_figures/eval_results/cellpose/cyto3/dsb_fixed.txt
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