├── .codecov.yml ├── .github ├── CONTRIBUTING.md ├── ISSUE_TEMPLATE │ ├── Bug_report.md │ └── Feature_request.md └── workflows │ └── ci-testing.yml ├── .gitignore ├── LICENSE ├── README.md ├── _config.yml ├── annotations ├── lung-lesion_1 │ └── user-PS_scale-50pc │ │ ├── 29-041-Izd2-w35-CD31-3-les1.csv │ │ ├── 29-041-Izd2-w35-Cc10-5-les1.csv │ │ ├── 29-041-Izd2-w35-He-les1.csv │ │ ├── 29-041-Izd2-w35-Ki67-7-les1.csv │ │ └── 29-041-Izd2-w35-proSPC-4-les1.csv ├── lung-lesion_2 │ └── user-PS_scale-50pc │ │ ├── 29-041-Izd2-w35-CD31-3-les2.csv │ │ ├── 29-041-Izd2-w35-Cc10-5-les2.csv │ │ ├── 29-041-Izd2-w35-He-les2.csv │ │ ├── 29-041-Izd2-w35-Ki67-7-les2.csv │ │ └── 29-041-Izd2-w35-proSPC-4-les2.csv ├── lung-lesion_3 │ ├── user-JB_scale-50pc │ │ ├── 29-041-Izd2-w35-He-les3.csv │ │ └── 29-041-Izd2-w35-proSPC-4-les3.csv │ └── user-PS_scale-50pc │ │ ├── 29-041-Izd2-w35-CD31-3-les3.csv │ │ ├── 29-041-Izd2-w35-Cc10-5-les3.csv │ │ ├── 29-041-Izd2-w35-He-les3.csv │ │ ├── 29-041-Izd2-w35-Ki67-7-les3.csv │ │ └── 29-041-Izd2-w35-proSPC-4-les3.csv ├── lung-lobes_1 │ └── user-PS_scale-100pc │ │ ├── 29-039-U-35W-Izd1-1-HE.csv │ │ ├── 29-039-U-35W-Izd1-2-cd31.csv │ │ ├── 29-039-U-35W-Izd1-3-Pro-SPC.csv │ │ ├── 29-039-U-35W-Izd1-4-cc10.csv │ │ └── 29-039-U-35W-Izd1-6-ki67.csv ├── lung-lobes_2 │ └── user-PS_scale-100pc │ │ ├── 29-039-U-35W-Izd2-1-HE.csv │ │ ├── 29-039-U-35W-Izd2-2-cd31.csv │ │ ├── 29-039-U-35W-Izd2-3-Pro-SPC.csv │ │ ├── 29-039-U-35W-Izd2-4-cc10.csv │ │ └── 29-039-U-35W-Izd2-6-ki67.csv ├── lung-lobes_3 │ ├── user-JB_scale-100pc │ │ └── 29-040-U-35W-Izd1-1-HE.csv │ └── user-PS_scale-100pc │ │ ├── 29-040-U-35W-Izd1-1-HE.csv │ │ ├── 29-040-U-35W-Izd1-2-cd31.csv │ │ ├── 29-040-U-35W-Izd1-3-Pro-SPC.csv │ │ ├── 29-040-U-35W-Izd1-4-cc10.csv │ │ └── 29-040-U-35W-Izd1-6-ki67.csv ├── lung-lobes_4 │ └── user-PS_scale-100pc │ │ ├── 29-040-U-35W-Izd2-1-HE.csv │ │ ├── 29-040-U-35W-Izd2-2-cd31.csv │ │ ├── 29-040-U-35W-Izd2-3-Pro-SPC.csv │ │ ├── 29-040-U-35W-Izd2-4-cc10.csv │ │ └── 29-040-U-35W-Izd2-6-ki67.csv ├── mammary-gland_1 │ ├── user-JB_scale-100pc │ │ ├── s1_37-HE_A4926-4L.csv │ │ └── s1_40-PR_A4926-4L.csv │ └── user-PS_scale-100pc │ │ ├── s1-39-HE_A4926-4L.csv │ │ ├── s1_36-CNEU_A4926-4L.csv │ │ ├── s1_37-HE_A4926-4L.csv │ │ ├── s1_38-ER-A4962-4L.csv │ │ └── s1_40-PR_A4926-4L.csv └── mammary-gland_2 │ ├── user-JB_scale-100pc │ ├── s2_63-HE_A4926-4L.csv │ └── s2_68-ER-A4962-4L.csv │ └── user-PS_scale-100pc │ ├── s2_60-CNEU_A4926-4L.csv │ ├── s2_61-HE_A4926-4L.csv │ ├── s2_62-ER_A4926-4L.csv │ ├── s2_63-HE_A4926-4L.csv │ ├── s2_64-PR_A4926-4L.csv │ ├── s2_66-CNEU_A4926-4L.csv │ ├── s2_67-HE_A4926-4L.csv │ ├── s2_68-ER-A4962-4L.csv │ └── s2_70-PR_A4926-4L.csv ├── dataset └── lung-lesion_3 │ └── scale-5pc │ ├── 29-041-Izd2-w35-CD31-3-les3.jpg │ ├── 29-041-Izd2-w35-Cc10-5-les3.jpg │ ├── 29-041-Izd2-w35-He-les3.jpg │ ├── 29-041-Izd2-w35-Ki67-7-les3.jpg │ └── 29-041-Izd2-w35-proSPC-4-les3.jpg ├── figures ├── PAIR___29-041-Izd2-w35-CD31-3-les3___AND___29-041-Izd2-w35-proSPC-4-les3.jpg ├── imagej-image-pair.jpg ├── images-landmarks.jpg ├── landmarks-overlaps-warped.jpg └── landmarks-zoom.jpg ├── handlers ├── __init__.py ├── multiPointSet_export.ijm ├── multiPointSet_import.ijm ├── resize_images.sh ├── run_evaluate_landmarks.py ├── run_generate_landmarks.py ├── run_visualise_landmarks.py ├── test_runs.py └── utilities.py ├── pytest.ini └── requirements.txt /.codecov.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Borda/dataset-histology-landmarks/HEAD/.codecov.yml -------------------------------------------------------------------------------- /.github/CONTRIBUTING.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Borda/dataset-histology-landmarks/HEAD/.github/CONTRIBUTING.md -------------------------------------------------------------------------------- /.github/ISSUE_TEMPLATE/Bug_report.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Borda/dataset-histology-landmarks/HEAD/.github/ISSUE_TEMPLATE/Bug_report.md -------------------------------------------------------------------------------- /.github/ISSUE_TEMPLATE/Feature_request.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Borda/dataset-histology-landmarks/HEAD/.github/ISSUE_TEMPLATE/Feature_request.md -------------------------------------------------------------------------------- /.github/workflows/ci-testing.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Borda/dataset-histology-landmarks/HEAD/.github/workflows/ci-testing.yml -------------------------------------------------------------------------------- /.gitignore: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Borda/dataset-histology-landmarks/HEAD/.gitignore -------------------------------------------------------------------------------- /LICENSE: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Borda/dataset-histology-landmarks/HEAD/LICENSE -------------------------------------------------------------------------------- /README.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Borda/dataset-histology-landmarks/HEAD/README.md -------------------------------------------------------------------------------- /_config.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Borda/dataset-histology-landmarks/HEAD/_config.yml -------------------------------------------------------------------------------- /annotations/lung-lesion_1/user-PS_scale-50pc/29-041-Izd2-w35-CD31-3-les1.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Borda/dataset-histology-landmarks/HEAD/annotations/lung-lesion_1/user-PS_scale-50pc/29-041-Izd2-w35-CD31-3-les1.csv -------------------------------------------------------------------------------- /annotations/lung-lesion_1/user-PS_scale-50pc/29-041-Izd2-w35-Cc10-5-les1.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Borda/dataset-histology-landmarks/HEAD/annotations/lung-lesion_1/user-PS_scale-50pc/29-041-Izd2-w35-Cc10-5-les1.csv -------------------------------------------------------------------------------- /annotations/lung-lesion_1/user-PS_scale-50pc/29-041-Izd2-w35-He-les1.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Borda/dataset-histology-landmarks/HEAD/annotations/lung-lesion_1/user-PS_scale-50pc/29-041-Izd2-w35-He-les1.csv -------------------------------------------------------------------------------- /annotations/lung-lesion_1/user-PS_scale-50pc/29-041-Izd2-w35-Ki67-7-les1.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Borda/dataset-histology-landmarks/HEAD/annotations/lung-lesion_1/user-PS_scale-50pc/29-041-Izd2-w35-Ki67-7-les1.csv -------------------------------------------------------------------------------- /annotations/lung-lesion_1/user-PS_scale-50pc/29-041-Izd2-w35-proSPC-4-les1.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Borda/dataset-histology-landmarks/HEAD/annotations/lung-lesion_1/user-PS_scale-50pc/29-041-Izd2-w35-proSPC-4-les1.csv -------------------------------------------------------------------------------- /annotations/lung-lesion_2/user-PS_scale-50pc/29-041-Izd2-w35-CD31-3-les2.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Borda/dataset-histology-landmarks/HEAD/annotations/lung-lesion_2/user-PS_scale-50pc/29-041-Izd2-w35-CD31-3-les2.csv -------------------------------------------------------------------------------- /annotations/lung-lesion_2/user-PS_scale-50pc/29-041-Izd2-w35-Cc10-5-les2.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Borda/dataset-histology-landmarks/HEAD/annotations/lung-lesion_2/user-PS_scale-50pc/29-041-Izd2-w35-Cc10-5-les2.csv -------------------------------------------------------------------------------- /annotations/lung-lesion_2/user-PS_scale-50pc/29-041-Izd2-w35-He-les2.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Borda/dataset-histology-landmarks/HEAD/annotations/lung-lesion_2/user-PS_scale-50pc/29-041-Izd2-w35-He-les2.csv -------------------------------------------------------------------------------- /annotations/lung-lesion_2/user-PS_scale-50pc/29-041-Izd2-w35-Ki67-7-les2.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Borda/dataset-histology-landmarks/HEAD/annotations/lung-lesion_2/user-PS_scale-50pc/29-041-Izd2-w35-Ki67-7-les2.csv -------------------------------------------------------------------------------- /annotations/lung-lesion_2/user-PS_scale-50pc/29-041-Izd2-w35-proSPC-4-les2.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Borda/dataset-histology-landmarks/HEAD/annotations/lung-lesion_2/user-PS_scale-50pc/29-041-Izd2-w35-proSPC-4-les2.csv -------------------------------------------------------------------------------- /annotations/lung-lesion_3/user-JB_scale-50pc/29-041-Izd2-w35-He-les3.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Borda/dataset-histology-landmarks/HEAD/annotations/lung-lesion_3/user-JB_scale-50pc/29-041-Izd2-w35-He-les3.csv -------------------------------------------------------------------------------- /annotations/lung-lesion_3/user-JB_scale-50pc/29-041-Izd2-w35-proSPC-4-les3.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Borda/dataset-histology-landmarks/HEAD/annotations/lung-lesion_3/user-JB_scale-50pc/29-041-Izd2-w35-proSPC-4-les3.csv -------------------------------------------------------------------------------- /annotations/lung-lesion_3/user-PS_scale-50pc/29-041-Izd2-w35-CD31-3-les3.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Borda/dataset-histology-landmarks/HEAD/annotations/lung-lesion_3/user-PS_scale-50pc/29-041-Izd2-w35-CD31-3-les3.csv -------------------------------------------------------------------------------- /annotations/lung-lesion_3/user-PS_scale-50pc/29-041-Izd2-w35-Cc10-5-les3.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Borda/dataset-histology-landmarks/HEAD/annotations/lung-lesion_3/user-PS_scale-50pc/29-041-Izd2-w35-Cc10-5-les3.csv -------------------------------------------------------------------------------- /annotations/lung-lesion_3/user-PS_scale-50pc/29-041-Izd2-w35-He-les3.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Borda/dataset-histology-landmarks/HEAD/annotations/lung-lesion_3/user-PS_scale-50pc/29-041-Izd2-w35-He-les3.csv -------------------------------------------------------------------------------- /annotations/lung-lesion_3/user-PS_scale-50pc/29-041-Izd2-w35-Ki67-7-les3.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Borda/dataset-histology-landmarks/HEAD/annotations/lung-lesion_3/user-PS_scale-50pc/29-041-Izd2-w35-Ki67-7-les3.csv -------------------------------------------------------------------------------- /annotations/lung-lesion_3/user-PS_scale-50pc/29-041-Izd2-w35-proSPC-4-les3.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Borda/dataset-histology-landmarks/HEAD/annotations/lung-lesion_3/user-PS_scale-50pc/29-041-Izd2-w35-proSPC-4-les3.csv -------------------------------------------------------------------------------- /annotations/lung-lobes_1/user-PS_scale-100pc/29-039-U-35W-Izd1-1-HE.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Borda/dataset-histology-landmarks/HEAD/annotations/lung-lobes_1/user-PS_scale-100pc/29-039-U-35W-Izd1-1-HE.csv -------------------------------------------------------------------------------- /annotations/lung-lobes_1/user-PS_scale-100pc/29-039-U-35W-Izd1-2-cd31.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Borda/dataset-histology-landmarks/HEAD/annotations/lung-lobes_1/user-PS_scale-100pc/29-039-U-35W-Izd1-2-cd31.csv -------------------------------------------------------------------------------- /annotations/lung-lobes_1/user-PS_scale-100pc/29-039-U-35W-Izd1-3-Pro-SPC.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Borda/dataset-histology-landmarks/HEAD/annotations/lung-lobes_1/user-PS_scale-100pc/29-039-U-35W-Izd1-3-Pro-SPC.csv -------------------------------------------------------------------------------- /annotations/lung-lobes_1/user-PS_scale-100pc/29-039-U-35W-Izd1-4-cc10.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Borda/dataset-histology-landmarks/HEAD/annotations/lung-lobes_1/user-PS_scale-100pc/29-039-U-35W-Izd1-4-cc10.csv -------------------------------------------------------------------------------- /annotations/lung-lobes_1/user-PS_scale-100pc/29-039-U-35W-Izd1-6-ki67.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Borda/dataset-histology-landmarks/HEAD/annotations/lung-lobes_1/user-PS_scale-100pc/29-039-U-35W-Izd1-6-ki67.csv -------------------------------------------------------------------------------- /annotations/lung-lobes_2/user-PS_scale-100pc/29-039-U-35W-Izd2-1-HE.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Borda/dataset-histology-landmarks/HEAD/annotations/lung-lobes_2/user-PS_scale-100pc/29-039-U-35W-Izd2-1-HE.csv -------------------------------------------------------------------------------- /annotations/lung-lobes_2/user-PS_scale-100pc/29-039-U-35W-Izd2-2-cd31.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Borda/dataset-histology-landmarks/HEAD/annotations/lung-lobes_2/user-PS_scale-100pc/29-039-U-35W-Izd2-2-cd31.csv -------------------------------------------------------------------------------- /annotations/lung-lobes_2/user-PS_scale-100pc/29-039-U-35W-Izd2-3-Pro-SPC.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Borda/dataset-histology-landmarks/HEAD/annotations/lung-lobes_2/user-PS_scale-100pc/29-039-U-35W-Izd2-3-Pro-SPC.csv -------------------------------------------------------------------------------- /annotations/lung-lobes_2/user-PS_scale-100pc/29-039-U-35W-Izd2-4-cc10.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Borda/dataset-histology-landmarks/HEAD/annotations/lung-lobes_2/user-PS_scale-100pc/29-039-U-35W-Izd2-4-cc10.csv -------------------------------------------------------------------------------- /annotations/lung-lobes_2/user-PS_scale-100pc/29-039-U-35W-Izd2-6-ki67.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Borda/dataset-histology-landmarks/HEAD/annotations/lung-lobes_2/user-PS_scale-100pc/29-039-U-35W-Izd2-6-ki67.csv -------------------------------------------------------------------------------- /annotations/lung-lobes_3/user-JB_scale-100pc/29-040-U-35W-Izd1-1-HE.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Borda/dataset-histology-landmarks/HEAD/annotations/lung-lobes_3/user-JB_scale-100pc/29-040-U-35W-Izd1-1-HE.csv -------------------------------------------------------------------------------- /annotations/lung-lobes_3/user-PS_scale-100pc/29-040-U-35W-Izd1-1-HE.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Borda/dataset-histology-landmarks/HEAD/annotations/lung-lobes_3/user-PS_scale-100pc/29-040-U-35W-Izd1-1-HE.csv -------------------------------------------------------------------------------- /annotations/lung-lobes_3/user-PS_scale-100pc/29-040-U-35W-Izd1-2-cd31.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Borda/dataset-histology-landmarks/HEAD/annotations/lung-lobes_3/user-PS_scale-100pc/29-040-U-35W-Izd1-2-cd31.csv -------------------------------------------------------------------------------- /annotations/lung-lobes_3/user-PS_scale-100pc/29-040-U-35W-Izd1-3-Pro-SPC.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Borda/dataset-histology-landmarks/HEAD/annotations/lung-lobes_3/user-PS_scale-100pc/29-040-U-35W-Izd1-3-Pro-SPC.csv -------------------------------------------------------------------------------- /annotations/lung-lobes_3/user-PS_scale-100pc/29-040-U-35W-Izd1-4-cc10.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Borda/dataset-histology-landmarks/HEAD/annotations/lung-lobes_3/user-PS_scale-100pc/29-040-U-35W-Izd1-4-cc10.csv -------------------------------------------------------------------------------- /annotations/lung-lobes_3/user-PS_scale-100pc/29-040-U-35W-Izd1-6-ki67.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Borda/dataset-histology-landmarks/HEAD/annotations/lung-lobes_3/user-PS_scale-100pc/29-040-U-35W-Izd1-6-ki67.csv -------------------------------------------------------------------------------- /annotations/lung-lobes_4/user-PS_scale-100pc/29-040-U-35W-Izd2-1-HE.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Borda/dataset-histology-landmarks/HEAD/annotations/lung-lobes_4/user-PS_scale-100pc/29-040-U-35W-Izd2-1-HE.csv -------------------------------------------------------------------------------- /annotations/lung-lobes_4/user-PS_scale-100pc/29-040-U-35W-Izd2-2-cd31.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Borda/dataset-histology-landmarks/HEAD/annotations/lung-lobes_4/user-PS_scale-100pc/29-040-U-35W-Izd2-2-cd31.csv -------------------------------------------------------------------------------- /annotations/lung-lobes_4/user-PS_scale-100pc/29-040-U-35W-Izd2-3-Pro-SPC.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Borda/dataset-histology-landmarks/HEAD/annotations/lung-lobes_4/user-PS_scale-100pc/29-040-U-35W-Izd2-3-Pro-SPC.csv -------------------------------------------------------------------------------- /annotations/lung-lobes_4/user-PS_scale-100pc/29-040-U-35W-Izd2-4-cc10.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Borda/dataset-histology-landmarks/HEAD/annotations/lung-lobes_4/user-PS_scale-100pc/29-040-U-35W-Izd2-4-cc10.csv -------------------------------------------------------------------------------- /annotations/lung-lobes_4/user-PS_scale-100pc/29-040-U-35W-Izd2-6-ki67.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Borda/dataset-histology-landmarks/HEAD/annotations/lung-lobes_4/user-PS_scale-100pc/29-040-U-35W-Izd2-6-ki67.csv -------------------------------------------------------------------------------- /annotations/mammary-gland_1/user-JB_scale-100pc/s1_37-HE_A4926-4L.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Borda/dataset-histology-landmarks/HEAD/annotations/mammary-gland_1/user-JB_scale-100pc/s1_37-HE_A4926-4L.csv -------------------------------------------------------------------------------- /annotations/mammary-gland_1/user-JB_scale-100pc/s1_40-PR_A4926-4L.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Borda/dataset-histology-landmarks/HEAD/annotations/mammary-gland_1/user-JB_scale-100pc/s1_40-PR_A4926-4L.csv -------------------------------------------------------------------------------- /annotations/mammary-gland_1/user-PS_scale-100pc/s1-39-HE_A4926-4L.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Borda/dataset-histology-landmarks/HEAD/annotations/mammary-gland_1/user-PS_scale-100pc/s1-39-HE_A4926-4L.csv -------------------------------------------------------------------------------- /annotations/mammary-gland_1/user-PS_scale-100pc/s1_36-CNEU_A4926-4L.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Borda/dataset-histology-landmarks/HEAD/annotations/mammary-gland_1/user-PS_scale-100pc/s1_36-CNEU_A4926-4L.csv -------------------------------------------------------------------------------- /annotations/mammary-gland_1/user-PS_scale-100pc/s1_37-HE_A4926-4L.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Borda/dataset-histology-landmarks/HEAD/annotations/mammary-gland_1/user-PS_scale-100pc/s1_37-HE_A4926-4L.csv -------------------------------------------------------------------------------- /annotations/mammary-gland_1/user-PS_scale-100pc/s1_38-ER-A4962-4L.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Borda/dataset-histology-landmarks/HEAD/annotations/mammary-gland_1/user-PS_scale-100pc/s1_38-ER-A4962-4L.csv -------------------------------------------------------------------------------- /annotations/mammary-gland_1/user-PS_scale-100pc/s1_40-PR_A4926-4L.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Borda/dataset-histology-landmarks/HEAD/annotations/mammary-gland_1/user-PS_scale-100pc/s1_40-PR_A4926-4L.csv -------------------------------------------------------------------------------- /annotations/mammary-gland_2/user-JB_scale-100pc/s2_63-HE_A4926-4L.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Borda/dataset-histology-landmarks/HEAD/annotations/mammary-gland_2/user-JB_scale-100pc/s2_63-HE_A4926-4L.csv -------------------------------------------------------------------------------- /annotations/mammary-gland_2/user-JB_scale-100pc/s2_68-ER-A4962-4L.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Borda/dataset-histology-landmarks/HEAD/annotations/mammary-gland_2/user-JB_scale-100pc/s2_68-ER-A4962-4L.csv -------------------------------------------------------------------------------- /annotations/mammary-gland_2/user-PS_scale-100pc/s2_60-CNEU_A4926-4L.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Borda/dataset-histology-landmarks/HEAD/annotations/mammary-gland_2/user-PS_scale-100pc/s2_60-CNEU_A4926-4L.csv -------------------------------------------------------------------------------- /annotations/mammary-gland_2/user-PS_scale-100pc/s2_61-HE_A4926-4L.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Borda/dataset-histology-landmarks/HEAD/annotations/mammary-gland_2/user-PS_scale-100pc/s2_61-HE_A4926-4L.csv -------------------------------------------------------------------------------- /annotations/mammary-gland_2/user-PS_scale-100pc/s2_62-ER_A4926-4L.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Borda/dataset-histology-landmarks/HEAD/annotations/mammary-gland_2/user-PS_scale-100pc/s2_62-ER_A4926-4L.csv -------------------------------------------------------------------------------- /annotations/mammary-gland_2/user-PS_scale-100pc/s2_63-HE_A4926-4L.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Borda/dataset-histology-landmarks/HEAD/annotations/mammary-gland_2/user-PS_scale-100pc/s2_63-HE_A4926-4L.csv -------------------------------------------------------------------------------- /annotations/mammary-gland_2/user-PS_scale-100pc/s2_64-PR_A4926-4L.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Borda/dataset-histology-landmarks/HEAD/annotations/mammary-gland_2/user-PS_scale-100pc/s2_64-PR_A4926-4L.csv -------------------------------------------------------------------------------- /annotations/mammary-gland_2/user-PS_scale-100pc/s2_66-CNEU_A4926-4L.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Borda/dataset-histology-landmarks/HEAD/annotations/mammary-gland_2/user-PS_scale-100pc/s2_66-CNEU_A4926-4L.csv -------------------------------------------------------------------------------- /annotations/mammary-gland_2/user-PS_scale-100pc/s2_67-HE_A4926-4L.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Borda/dataset-histology-landmarks/HEAD/annotations/mammary-gland_2/user-PS_scale-100pc/s2_67-HE_A4926-4L.csv -------------------------------------------------------------------------------- /annotations/mammary-gland_2/user-PS_scale-100pc/s2_68-ER-A4962-4L.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Borda/dataset-histology-landmarks/HEAD/annotations/mammary-gland_2/user-PS_scale-100pc/s2_68-ER-A4962-4L.csv -------------------------------------------------------------------------------- /annotations/mammary-gland_2/user-PS_scale-100pc/s2_70-PR_A4926-4L.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Borda/dataset-histology-landmarks/HEAD/annotations/mammary-gland_2/user-PS_scale-100pc/s2_70-PR_A4926-4L.csv -------------------------------------------------------------------------------- /dataset/lung-lesion_3/scale-5pc/29-041-Izd2-w35-CD31-3-les3.jpg: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Borda/dataset-histology-landmarks/HEAD/dataset/lung-lesion_3/scale-5pc/29-041-Izd2-w35-CD31-3-les3.jpg -------------------------------------------------------------------------------- /dataset/lung-lesion_3/scale-5pc/29-041-Izd2-w35-Cc10-5-les3.jpg: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Borda/dataset-histology-landmarks/HEAD/dataset/lung-lesion_3/scale-5pc/29-041-Izd2-w35-Cc10-5-les3.jpg -------------------------------------------------------------------------------- /dataset/lung-lesion_3/scale-5pc/29-041-Izd2-w35-He-les3.jpg: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Borda/dataset-histology-landmarks/HEAD/dataset/lung-lesion_3/scale-5pc/29-041-Izd2-w35-He-les3.jpg -------------------------------------------------------------------------------- /dataset/lung-lesion_3/scale-5pc/29-041-Izd2-w35-Ki67-7-les3.jpg: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Borda/dataset-histology-landmarks/HEAD/dataset/lung-lesion_3/scale-5pc/29-041-Izd2-w35-Ki67-7-les3.jpg -------------------------------------------------------------------------------- /dataset/lung-lesion_3/scale-5pc/29-041-Izd2-w35-proSPC-4-les3.jpg: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Borda/dataset-histology-landmarks/HEAD/dataset/lung-lesion_3/scale-5pc/29-041-Izd2-w35-proSPC-4-les3.jpg -------------------------------------------------------------------------------- /figures/PAIR___29-041-Izd2-w35-CD31-3-les3___AND___29-041-Izd2-w35-proSPC-4-les3.jpg: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Borda/dataset-histology-landmarks/HEAD/figures/PAIR___29-041-Izd2-w35-CD31-3-les3___AND___29-041-Izd2-w35-proSPC-4-les3.jpg -------------------------------------------------------------------------------- /figures/imagej-image-pair.jpg: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Borda/dataset-histology-landmarks/HEAD/figures/imagej-image-pair.jpg -------------------------------------------------------------------------------- /figures/images-landmarks.jpg: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Borda/dataset-histology-landmarks/HEAD/figures/images-landmarks.jpg -------------------------------------------------------------------------------- /figures/landmarks-overlaps-warped.jpg: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Borda/dataset-histology-landmarks/HEAD/figures/landmarks-overlaps-warped.jpg -------------------------------------------------------------------------------- /figures/landmarks-zoom.jpg: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Borda/dataset-histology-landmarks/HEAD/figures/landmarks-zoom.jpg -------------------------------------------------------------------------------- /handlers/__init__.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Borda/dataset-histology-landmarks/HEAD/handlers/__init__.py -------------------------------------------------------------------------------- /handlers/multiPointSet_export.ijm: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Borda/dataset-histology-landmarks/HEAD/handlers/multiPointSet_export.ijm -------------------------------------------------------------------------------- /handlers/multiPointSet_import.ijm: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Borda/dataset-histology-landmarks/HEAD/handlers/multiPointSet_import.ijm -------------------------------------------------------------------------------- /handlers/resize_images.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Borda/dataset-histology-landmarks/HEAD/handlers/resize_images.sh -------------------------------------------------------------------------------- /handlers/run_evaluate_landmarks.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Borda/dataset-histology-landmarks/HEAD/handlers/run_evaluate_landmarks.py -------------------------------------------------------------------------------- /handlers/run_generate_landmarks.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Borda/dataset-histology-landmarks/HEAD/handlers/run_generate_landmarks.py -------------------------------------------------------------------------------- /handlers/run_visualise_landmarks.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Borda/dataset-histology-landmarks/HEAD/handlers/run_visualise_landmarks.py -------------------------------------------------------------------------------- /handlers/test_runs.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Borda/dataset-histology-landmarks/HEAD/handlers/test_runs.py -------------------------------------------------------------------------------- /handlers/utilities.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Borda/dataset-histology-landmarks/HEAD/handlers/utilities.py -------------------------------------------------------------------------------- /pytest.ini: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Borda/dataset-histology-landmarks/HEAD/pytest.ini -------------------------------------------------------------------------------- /requirements.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Borda/dataset-histology-landmarks/HEAD/requirements.txt --------------------------------------------------------------------------------