./.codecov.yml .gitattributes LICENSE MANIFEST.in birl/__init__.py birl/benchmark.py birl/bm_template.py birl/utilities/__init__.py birl/utilities/data_io.py birl/utilities/dataset.py birl/utilities/drawing.py birl/utilities/evaluate.py birl/utilities/experiments.py birl/utilities/registration.py bm_ANHIR/Dockerfile bm_ANHIR/__init__.py bm_ANHIR/copy_sub-scales.py bm_ANHIR/evaluate_submission.py bm_ANHIR/generate_regist_pairs.py bm_ANHIR/send_notification_mail.py bm_ANHIR/zip_dataset_by_cover.py bm_CIMA/results_size-10k.zip bm_CIMA/results_size-full.zip bm_CIMA/run-SOTA-experiments.sh bm_dataset/__init__.py bm_dataset/convert_tiff2png.py bm_dataset/create_real_synth_dataset.py bm_dataset/crop_tissue_images.py bm_dataset/generate_regist_pairs.py bm_dataset/rescale_tissue_images.py bm_dataset/rescale_tissue_landmarks.py bm_dataset/split_images_two_tissues.py bm_experiments/Dockerfile bm_experiments/__init__.py bm_experiments/bm_ANTs.py bm_experiments/bm_ANTsPy.py bm_experiments/bm_DROP.py bm_experiments/bm_DROP2.py bm_experiments/bm_RVSS.py bm_experiments/bm_bUnwarpJ.py bm_experiments/bm_comp_perform.py bm_experiments/bm_elastix.py bm_experiments/bm_rNiftyReg.py bm_experiments/evaluate_experiment.py bm_experiments/run-all-experiments.sh data-images/landmarks/artificial_moving-affine.pts data-images/landmarks/artificial_moving-elastic.pts data-images/landmarks/artificial_moving-rigid.pts data-images/landmarks/artificial_reference.pts data-images/lesions_/scale-5pc/Izd2-29-041-w35_HE.pts data-images/lesions_/scale-5pc/Izd2-29-041-w35_proSPC.pts data-images/rat-kidney_/scale-5pc/Rat-Kidney_HE.pts data-images/rat-kidney_/scale-5pc/Rat-Kidney_PanCytokeratin.pts docs/Makefile docs/references.bib docs/source/ANHIR.rst docs/source/conf.py docs/source/index.rst notebooks/ANHIR_evaluation-board.ipynb notebooks/ANHIR_submissions-stat.ipynb notebooks/CIMA_SOTA-results_comparing.ipynb notebooks/CIMA_SOTA-results_scope.ipynb scripts/ImageJ/apply-RVSS-registration.bsh scripts/ImageJ/apply-RVSS-transform.bsh scripts/ImageJ/apply-SIFT-bUnwarpJ-registration.bsh scripts/ImageJ/apply-bUnwarpJ-registration.bsh scripts/ImageJ/apply-bUnwarpJ-transform.bsh scripts/ImageJ/histogram-matching-for-macro.bsh scripts/ImageJ/histogram-matching.bsh scripts/ImageJ/makeImageMosaic.ijm scripts/ImageJ/multiPointSet_export.ijm scripts/ImageJ/multiPointSet_import.ijm scripts/Python/run_ANTsPy.py scripts/Python/run_SimpleElastix.py scripts/Python/run_SimpleITK.py scripts/Rscript/RNiftyReg_elastic.r scripts/Rscript/RNiftyReg_linear.r setup.cfg setup.py tests/test_benchmark.py tests/test_data-utils.py <<<<<< network # path=coverage.xml /Users/runner/work/BIRL/BIRL <<<<<< EOF