diff --git a/notebooks/.ipynb_checkpoints/bim_stats-checkpoint.ipynb b/notebooks/.ipynb_checkpoints/bim_stats-checkpoint.ipynb deleted file mode 100644 index 9a8c80e..0000000 --- a/notebooks/.ipynb_checkpoints/bim_stats-checkpoint.ipynb +++ /dev/null @@ -1,1243 +0,0 @@ -{ - "cells": [ - { - "cell_type": "code", - "execution_count": 44, - "id": "a7daa401", - "metadata": {}, - "outputs": [], - "source": [ - "import pandas as pd\n", - "import seaborn as sns\n", - "import matplotlib.pyplot as plt\n", - "import io\n", - "sns.set(rc={'figure.figsize':(11,8)})" - ] - }, - { - "cell_type": "code", - "execution_count": 45, - "id": "4a8cd87c", - "metadata": {}, - "outputs": [ - { - "data": { - "text/html": [ - "
\n", - " | Medical Imaging Modality | \n", - "Biomed Task | \n", - "ML Task | \n", - "License | \n", - "Performance | \n", - "Supervised | \n", - "Parameters download | \n", - "Reference | \n", - "Link to model | \n", - "Link to dataset | \n", - "Parameters link | \n", - "Comment | \n", - "
---|---|---|---|---|---|---|---|---|---|---|---|---|
0 | \n", - "3D microscopy | \n", - "Nuclei detection | \n", - "Segmentation | \n", - "MIT | \n", - "0.937 AP | \n", - "True | \n", - "False | \n", - "Hirsch, Peter, and Dagmar Kainmueller. \"An aux... | \n", - "https://github.com/Kainmueller-Lab/aux_cpv_loss | \n", - "https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2... | \n", - "N/a | \n", - "dataset comes from private support of another ... | \n", - "
1 | \n", - "Confocal microscopy | \n", - "Cellular structures reconstruction | \n", - "Reconstruction | \n", - "Apache-2.0 | \n", - "0.87 SSIM | \n", - "True | \n", - "False | \n", - "Vizcaino, Josue Page, et al. \"Learning to Reco... | \n", - "https://github.com/pvjosue/LFMNet | \n", - "N/a | \n", - "N/a | \n", - "34.45 PSNR, 0.87 SSIM | \n", - "
2 | \n", - "Cryo-electron microscopy | \n", - "Cellular structures reconstruction | \n", - "Reconstruction | \n", - "GPL-3.0 | \n", - "2.5 Reconstruction accuracy | \n", - "False | \n", - "False | \n", - "Zhong, E. D., Bepler, T., Davis, J. H., & Berg... | \n", - "https://github.com/zhonge/cryodrgn | \n", - "https://www.ebi.ac.uk/empiar/EMPIAR-10076/ | \n", - "N/a | \n", - "GAN | \n", - "
3 | \n", - "Cryo-electron microscopy | \n", - "Protein structures reconstruction | \n", - "Reconstruction | \n", - "GPL-3.0 | \n", - "5.82 Angstrom | \n", - "True | \n", - "False | \n", - "Ullrich, K., Berg, R. V. D., Brubaker, M., Fle... | \n", - "https://github.com/KarenUllrich/pytorch-backpr... | \n", - "https://github.com/KarenUllrich/Pytorch-Backpr... | \n", - "N/a | \n", - "Validate the backpropagation with FSC | \n", - "
4 | \n", - "CT | \n", - "Kidney tumor | \n", - "Segmentation | \n", - "GPL-3.0 | \n", - "0.95 Dice | \n", - "True | \n", - "False | \n", - "Müller, D., & Kramer, F. (2021). MIScnn: a fra... | \n", - "https://github.com/frankkramer-lab/MIScnn | \n", - "https://github.com/neheller/kits19, https://d... | \n", - "N/a | \n", - "Dice coefficient median 0.9544 for kidney Segm... | \n", - "
\n", - " | Medical Imaging Modality | \n", - "Biomed Task | \n", - "ML Task | \n", - "License | \n", - "Performance | \n", - "Supervised | \n", - "Parameters download | \n", - "Reference | \n", - "Link to model | \n", - "Link to dataset | \n", - "Parameters link | \n", - "Comment | \n", - "Parameters storage | \n", - "Data download | \n", - "
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
0 | \n", - "3D microscopy | \n", - "Nuclei detection | \n", - "Segmentation | \n", - "MIT | \n", - "0.937 AP | \n", - "True | \n", - "False | \n", - "Hirsch, Peter, and Dagmar Kainmueller. \"An aux... | \n", - "https://github.com/Kainmueller-Lab/aux_cpv_loss | \n", - "https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2... | \n", - "N/a | \n", - "dataset comes from private support of another ... | \n", - "N/a | \n", - "True | \n", - "
1 | \n", - "Confocal microscopy | \n", - "Cellular structures reconstruction | \n", - "Reconstruction | \n", - "Apache-2.0 | \n", - "0.87 SSIM | \n", - "True | \n", - "False | \n", - "Vizcaino, Josue Page, et al. \"Learning to Reco... | \n", - "https://github.com/pvjosue/LFMNet | \n", - "N/a | \n", - "N/a | \n", - "34.45 PSNR, 0.87 SSIM | \n", - "N/a | \n", - "False | \n", - "
2 | \n", - "Cryo-electron microscopy | \n", - "Cellular structures reconstruction | \n", - "Reconstruction | \n", - "GPL-3.0 | \n", - "2.5 Reconstruction accuracy | \n", - "False | \n", - "False | \n", - "Zhong, E. D., Bepler, T., Davis, J. H., & Berg... | \n", - "https://github.com/zhonge/cryodrgn | \n", - "https://www.ebi.ac.uk/empiar/EMPIAR-10076/ | \n", - "N/a | \n", - "GAN | \n", - "N/a | \n", - "True | \n", - "
3 | \n", - "Cryo-electron microscopy | \n", - "Protein structures reconstruction | \n", - "Reconstruction | \n", - "GPL-3.0 | \n", - "5.82 Angstrom | \n", - "True | \n", - "False | \n", - "Ullrich, K., Berg, R. V. D., Brubaker, M., Fle... | \n", - "https://github.com/KarenUllrich/pytorch-backpr... | \n", - "https://github.com/KarenUllrich/Pytorch-Backpr... | \n", - "N/a | \n", - "Validate the backpropagation with FSC | \n", - "N/a | \n", - "True | \n", - "
4 | \n", - "CT | \n", - "Kidney tumor | \n", - "Segmentation | \n", - "GPL-3.0 | \n", - "0.95 Dice | \n", - "True | \n", - "False | \n", - "Müller, D., & Kramer, F. (2021). MIScnn: a fra... | \n", - "https://github.com/frankkramer-lab/MIScnn | \n", - "https://github.com/neheller/kits19, https://d... | \n", - "N/a | \n", - "Dice coefficient median 0.9544 for kidney Segm... | \n", - "N/a | \n", - "True | \n", - "
\n", - " | Medical Imaging Modality | \n", - "Biomed Task | \n", - "ML Task | \n", - "License | \n", - "Performance | \n", - "Supervised | \n", - "Parameters download | \n", - "Reference | \n", - "Link to model | \n", - "Link to dataset | \n", - "Parameters link | \n", - "Comment | \n", - "Parameters storage | \n", - "Data download | \n", - "
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
11 | \n", - "CT | \n", - "Pulmonary nodule | \n", - "Segmentation | \n", - "CC BY-NC-SA 4.0 | \n", - "0.55 IoU | \n", - "True | \n", - "True | \n", - "Aresta, G., Jacobs, C., Araújo, T., Cunha, A.,... | \n", - "https://github.com/gmaresta/iW-Net | \n", - "https://wiki.cancerimagingarchive.net/display/... | \n", - "https://github.com/gmaresta/iW-Net/blob/master... | \n", - "NaN | \n", - "GitHub | \n", - "True | \n", - "
18 | \n", - "Dermatoscopy | \n", - "Skin tumor | \n", - "Classification | \n", - "MIT | \n", - "0.81 AUC | \n", - "True | \n", - "True | \n", - "Zunair, H., & Hamza, A. B. (2020). Melanoma de... | \n", - "https://github.com/hasibzunair/adversarial-les... | \n", - "https://challenge.isic-archive.com/data | \n", - "https://github.com/hasibzunair/adversarial-les... | \n", - "NaN | \n", - "GitHub | \n", - "True | \n", - "
22 | \n", - "Mammography | \n", - "Breast tumor | \n", - "Classification | \n", - "CC BY-NC-ND 4.0 | \n", - "0.93 AUC | \n", - "True | \n", - "True | \n", - "Shen, Y., Wu, N., Phang, J., Park, J., Liu, K.... | \n", - "https://github.com/nyukat/GMIC | \n", - "N/a | \n", - "https://github.com/nyukat/GMIC/tree/master/models | \n", - "Weakly supervised | \n", - "GitHub | \n", - "False | \n", - "
24 | \n", - "Mammography | \n", - "Breast tumor | \n", - "Classification | \n", - "CC BY-NC-SA 4.0 | \n", - "0.84 Accuracy | \n", - "True | \n", - "True | \n", - "Shen, L., Margolies, L. R., Rothstein, J. H., ... | \n", - "https://github.com/lishen/end2end-all-conv | \n", - "https://www.kaggle.com/datasets/awsaf49/cbis-d... | \n", - "https://drive.google.com/drive/folders/0B1PVLa... | \n", - "83.5% accuracy for single Model AUC, 86% accur... | \n", - "Google drive | \n", - "True | \n", - "
25 | \n", - "Digital Pathology | \n", - "Breast tumor | \n", - "Classification | \n", - "MIT | \n", - "0.93 Accuracy | \n", - "True | \n", - "True | \n", - "Rakhlin, A., Shvets, A., Iglovikov, V., & Kali... | \n", - "https://github.com/alexander-rakhlin/ICIAR2018 | \n", - "https://rdm.inesctec.pt/dataset/nis-2017-003 | \n", - "https://www.dropbox.com/s/oklwgz5v9suyj1k/ICIA... | \n", - "93.8% accuracy, AUC 97.3%, and sensitivity/spe... | \n", - "Dropbox | \n", - "True | \n", - "
\n", - " | Medical Imaging Modality | \n", - "Biomed Task | \n", - "ML Task | \n", - "License | \n", - "Performance | \n", - "Supervised | \n", - "Parameters download | \n", - "Reference | \n", - "Link to model | \n", - "Link to dataset | \n", - "Parameters link | \n", - "Comment | \n", - "Parameters storage | \n", - "Data download | \n", - "
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
1 | \n", - "Confocal microscopy | \n", - "Cellular structures reconstruction | \n", - "Reconstruction | \n", - "Apache-2.0 | \n", - "0.87 SSIM | \n", - "True | \n", - "False | \n", - "Vizcaino, Josue Page, et al. \"Learning to Reco... | \n", - "https://github.com/pvjosue/LFMNet | \n", - "N/a | \n", - "N/a | \n", - "34.45 PSNR, 0.87 SSIM | \n", - "N/a | \n", - "False | \n", - "
2 | \n", - "Cryo-electron microscopy | \n", - "Cellular structures reconstruction | \n", - "Reconstruction | \n", - "GPL-3.0 | \n", - "2.5 Reconstruction accuracy | \n", - "False | \n", - "False | \n", - "Zhong, E. D., Bepler, T., Davis, J. H., & Berg... | \n", - "https://github.com/zhonge/cryodrgn | \n", - "https://www.ebi.ac.uk/empiar/EMPIAR-10076/ | \n", - "N/a | \n", - "GAN | \n", - "N/a | \n", - "True | \n", - "
3 | \n", - "Cryo-electron microscopy | \n", - "Protein structures reconstruction | \n", - "Reconstruction | \n", - "GPL-3.0 | \n", - "5.82 Angstrom | \n", - "True | \n", - "False | \n", - "Ullrich, K., Berg, R. V. D., Brubaker, M., Fle... | \n", - "https://github.com/KarenUllrich/pytorch-backpr... | \n", - "https://github.com/KarenUllrich/Pytorch-Backpr... | \n", - "N/a | \n", - "Validate the backpropagation with FSC | \n", - "N/a | \n", - "True | \n", - "
14 | \n", - "CT | \n", - "Pulmonary nodule | \n", - "Detection | \n", - "Apache-2.0 | \n", - "0.76 FROC AUC | \n", - "True | \n", - "False | \n", - "Zhu, W., Vang, Y. S., Huang, Y., & Xie, X. (20... | \n", - "https://github.com/uci-cbcl/DeepEM-for-Weakly-... | \n", - "https://biometry.nci.nih.gov/cdas/nlst/ , http... | \n", - "N/a | \n", - "Average FROC 76% for DeepEM(Map) and 76.4% for... | \n", - "N/a | \n", - "True | \n", - "
15 | \n", - "CT | \n", - "Pulmonary nodule | \n", - "Detection | \n", - "MIT | \n", - "0.86 FROC AUC | \n", - "True | \n", - "False | \n", - "Li, Y., & Fan, Y. (2020, April). DeepSEED: 3D ... | \n", - "https://github.com/ymli39/DeepSEED-3D-ConvNets... | \n", - "https://luna16.grand-challenge.org/data , http... | \n", - "N/a | \n", - "FROC 86.2% on LUNA16 dataset and 77.3% on LIDC... | \n", - "N/a | \n", - "True | \n", - "
26 | \n", - "Mammography | \n", - "Breast tumor | \n", - "Image Inpainting & Data generation | \n", - "CC BY-NC-ND 4.0 | \n", - "0.896 AUC | \n", - "False | \n", - "True | \n", - "Wu, E., Wu, K., Cox, D., & Lotter, W. (2018). ... | \n", - "https://github.com/ericwu09/mammo-cigan | \n", - "https://wiki.cancerimagingarchive.net/display/... | \n", - "https://github.com/CQFIO/PhotographicImageSynt... | \n", - "NaN | \n", - "GitHub | \n", - "True | \n", - "
31 | \n", - "Digital Pathology | \n", - "Multiple pathologies | \n", - "Graph embedding | \n", - "AGPL 3.0 | \n", - "N/a | \n", - "False | \n", - "False | \n", - "Jaume, G., Pati, P., Anklin, V., Foncubierta, ... | \n", - "https://github.com/histocartography/histocarto... | \n", - "N/a | \n", - "N/a | \n", - "Plug and play modules | \n", - "N/a | \n", - "False | \n", - "
34 | \n", - "Electron microscopy | \n", - "Cellular structures reconstruction | \n", - "Reconstruction | \n", - "N/a | \n", - "0.446 IoU | \n", - "True | \n", - "False | \n", - "Guay, M. D., Emam, Z. A., Anderson, A. B., Aro... | \n", - "https://github.com/leapmanlab/examples | \n", - "https://leapmanlab.github.io/dense-cell/ | \n", - "N/a | \n", - "private dataset from NIBIB, NIH | \n", - "N/a | \n", - "True | \n", - "
35 | \n", - "Fluorescence microscopy | \n", - "Cellular structures reconstruction | \n", - "Image Inpainting & Data generation | \n", - "Apache-2.0 | \n", - "0.71 Quality Score | \n", - "False | \n", - "False | \n", - "Eschweiler, D., Rethwisch, M., Jarchow, M., Ko... | \n", - "https://github.com/stegmaierj/CellSynthesis | \n", - "NaN | \n", - "N/a | \n", - "GAN for data generation in 3D microscopy; Data... | \n", - "N/a | \n", - "True | \n", - "
39 | \n", - "Mammography | \n", - "Breast tumor | \n", - "Classification & Detection | \n", - "N/a | \n", - "0.95 AUC | \n", - "True | \n", - "True | \n", - "Ribli, D., Horváth, A., Unger, Z., Pollner, P.... | \n", - "https://github.com/riblidezso/frcnn_cad | \n", - "http://marathon.csee.usf.edu/Mammography/Datab... | \n", - "http://dkrib.web.elte.hu/cad_faster_rcnn/vgg16... | \n", - "Two of the three datasets available on request... | \n", - "N/a | \n", - "True | \n", - "
47 | \n", - "3D microscopy | \n", - "Image acquisition | \n", - "Reconstruction | \n", - "BSD-3-Clause | \n", - "30x Speed | \n", - "True | \n", - "False | \n", - "Saha, D., Schmidt, U., Zhang, Q., Barbotin, A.... | \n", - "https://github.com/mpicbg-csbd/phasenet | \n", - "https://github.com/mpicbg-csbd/phasenet | \n", - "N/a | \n", - "NaN | \n", - "N/a | \n", - "True | \n", - "