LICENSE
MANIFEST.in
README.md
pyproject.toml
cellbin2/__init__.py
cellbin2/cellbin_pipeline.py
cellbin2.egg-info/PKG-INFO
cellbin2.egg-info/SOURCES.txt
cellbin2.egg-info/dependency_links.txt
cellbin2.egg-info/requires.txt
cellbin2.egg-info/top_level.txt
cellbin2/config/Stereo-CITE_T_FF.json
cellbin2/config/Stereo-CITE_T_FF_R.json
cellbin2/config/Stereo-seq_N_FFPE.json
cellbin2/config/Stereo-seq_N_FFPE_R.json
cellbin2/config/Stereo-seq_T_FF.json
cellbin2/config/Stereo-seq_T_FF_R.json
cellbin2/config/cellbin.yaml
cellbin2/config/chip_mask.json
cellbin2/config/weights_url.json
cellbin2/contrib/__init__.py
cellbin2/contrib/base_module.py
cellbin2/contrib/calibration.py
cellbin2/contrib/cell_filter.py
cellbin2/contrib/cell_segmentor.py
cellbin2/contrib/cellpose_segmentor.py
cellbin2/contrib/chip_detector.py
cellbin2/contrib/chip_transform.py
cellbin2/contrib/clarity.py
cellbin2/contrib/fast_correct.py
cellbin2/contrib/gmm_correct.py
cellbin2/contrib/mask_manager.py
cellbin2/contrib/multimodal_cell_merge.py
cellbin2/contrib/param.py
cellbin2/contrib/tissue_segmentor.py
cellbin2/contrib/track_align.py
cellbin2/contrib/alignment/__init__.py
cellbin2/contrib/alignment/basic.py
cellbin2/contrib/alignment/chip_box.py
cellbin2/contrib/alignment/template_00pt.py
cellbin2/contrib/alignment/template_centroid.py
cellbin2/contrib/stitch/setup.py
cellbin2/contrib/stitch/mfws/__init__.py
cellbin2/contrib/stitch/mfws/main.py
cellbin2/contrib/stitch/mfws/modules/__init__.py
cellbin2/contrib/stitch/mfws/modules/fov_aligner.py
cellbin2/contrib/stitch/mfws/modules/global_location.py
cellbin2/contrib/stitch/mfws/modules/jitter_correct.py
cellbin2/contrib/stitch/mfws/modules/scan_method.py
cellbin2/contrib/stitch/mfws/modules/stitching.py
cellbin2/contrib/stitch/mfws/modules/wsi_stitch.py
cellbin2/contrib/template/__init__.py
cellbin2/contrib/template/inference.py
cellbin2/contrib/template/point_detector.py
cellbin2/contrib/template/track_qc.py
cellbin2/contrib/template/inferencev1/__init__.py
cellbin2/contrib/template/inferencev1/inference_v1.py
cellbin2/contrib/template/inferencev1/line_detector.py
cellbin2/contrib/template/inferencev1/roi_picker.py
cellbin2/contrib/template/inferencev1/template_match.py
cellbin2/contrib/template/inferencev1/track_line.py
cellbin2/contrib/template/inferencev2/__init__.py
cellbin2/contrib/template/inferencev2/inference_v2.py
cellbin2/contrib/template/inferencev2/rotate_search.py
cellbin2/contrib/template/inferencev2/scale_search.py
cellbin2/dnn/__init__.py
cellbin2/dnn/onnx_net.py
cellbin2/dnn/tensorrt_net.py
cellbin2/dnn/classify/__init__.py
cellbin2/dnn/classify/onnx_mobilenet3.py
cellbin2/dnn/detector/__init__.py
cellbin2/dnn/detector/onnx_yolo5_obb.py
cellbin2/dnn/detector/onnx_yolo8.py
cellbin2/dnn/detector/onnx_yolo8_obb.py
cellbin2/dnn/detector/util.py
cellbin2/dnn/segmentor/__init__.py
cellbin2/dnn/segmentor/cell_trace.py
cellbin2/dnn/segmentor/detector.py
cellbin2/dnn/segmentor/postprocess.py
cellbin2/dnn/segmentor/predict.py
cellbin2/dnn/segmentor/preprocess.py
cellbin2/dnn/segmentor/processing.py
cellbin2/dnn/segmentor/utils.py
cellbin2/dnn/tissue_segmentor/__init__.py
cellbin2/dnn/tissue_segmentor/big_chip_postprocess.py
cellbin2/dnn/tissue_segmentor/big_chip_preprocess.py
cellbin2/dnn/tissue_segmentor/detector.py
cellbin2/dnn/tissue_segmentor/postprocess.py
cellbin2/dnn/tissue_segmentor/preprocess.py
cellbin2/dnn/tissue_segmentor/processing.py
cellbin2/dnn/tissue_segmentor/utils.py
cellbin2/image/__init__.py
cellbin2/image/augmentation.py
cellbin2/image/mask.py
cellbin2/image/morphology.py
cellbin2/image/threshold.py
cellbin2/image/transform.py
cellbin2/image/wsi_split.py
cellbin2/matrix/__init__.py
cellbin2/matrix/box_detect.py
cellbin2/matrix/index_points_detect.py
cellbin2/matrix/matrix.py
cellbin2/modules/__init__.py
cellbin2/modules/analyze.py
cellbin2/modules/image_qc.py
cellbin2/modules/matrix_qc.py
cellbin2/modules/metadata.py
cellbin2/modules/metrics.py
cellbin2/modules/naming.py
cellbin2/modules/report_m.py
cellbin2/modules/run_state.py
cellbin2/modules/scheduler.py
cellbin2/modules/extract/__init__.py
cellbin2/modules/extract/cell_seg.py
cellbin2/modules/extract/matrix_extract.py
cellbin2/modules/extract/qc.py
cellbin2/modules/extract/register.py
cellbin2/modules/extract/tissue_seg.py
cellbin2/modules/extract/transform.py
cellbin2/modules/manual/__init__.py
cellbin2/modules/manual/manual_registration.py
cellbin2/modules/report/__init__.py
cellbin2/modules/report/index.html
cellbin2/modules/report/index_savecode.html
cellbin2/modules/report/min_html.py
cellbin2/modules/report/assets/common/Sorting icons.psd
cellbin2/modules/report/assets/common/favicon.ico
cellbin2/modules/report/assets/common/favicon.png
cellbin2/modules/report/assets/common/logo.png
cellbin2/modules/report/assets/common/sort_asc.png
cellbin2/modules/report/assets/common/sort_asc_disabled.png
cellbin2/modules/report/assets/common/sort_both.png
cellbin2/modules/report/assets/common/sort_desc.png
cellbin2/modules/report/assets/common/sort_desc_disabled.png
cellbin2/modules/report/assets/image/ssDNA_cell_intensity.png
cellbin2/modules/report/assets/image/ssDNA_chipbox.png
cellbin2/modules/report/assets/image/ssDNA_clarity.png
cellbin2/modules/report/assets/image/ssDNA_trackpoint.png
cellbin2/modules/report/assets/protein/adjusted/Adjusted_Gene_type.png
cellbin2/modules/report/assets/protein/adjusted/CellArea.png
cellbin2/modules/report/assets/protein/adjusted/GeneType.png
cellbin2/modules/report/assets/protein/adjusted/MIDCount.png
cellbin2/modules/report/assets/protein/adjusted/MID_counts.png
cellbin2/modules/report/assets/protein/adjusted/celldensity.png
cellbin2/modules/report/assets/protein/cellbin/CellArea.png
cellbin2/modules/report/assets/protein/cellbin/CellBin_MID_counts.png
cellbin2/modules/report/assets/protein/cellbin/GeneType.png
cellbin2/modules/report/assets/protein/cellbin/MIDCount.png
cellbin2/modules/report/assets/protein/cellbin/MID_counts.png
cellbin2/modules/report/assets/protein/cellbin/celldensity.png
cellbin2/modules/report/assets/rna/adjusted/Adjusted_Gene_type.png
cellbin2/modules/report/assets/rna/adjusted/CellArea.png
cellbin2/modules/report/assets/rna/adjusted/GeneType.png
cellbin2/modules/report/assets/rna/adjusted/MIDCount.png
cellbin2/modules/report/assets/rna/adjusted/MID_counts.png
cellbin2/modules/report/assets/rna/adjusted/celldensity.png
cellbin2/modules/report/assets/rna/cellbin/CellArea.png
cellbin2/modules/report/assets/rna/cellbin/GeneType.png
cellbin2/modules/report/assets/rna/cellbin/MIDCount.png
cellbin2/modules/report/assets/rna/cellbin/MID_counts.png
cellbin2/modules/report/assets/rna/cellbin/celldensity.png
cellbin2/modules/report/css/element-plus.min.css
cellbin2/modules/report/css/element-plus.stereo.css
cellbin2/modules/report/css/jquery.dataTables.css
cellbin2/modules/report/js/result.js
cellbin2/modules/report/js/result_template.js
cellbin2/modules/report/js/result_template_savecode.js
cellbin2/modules/report/js/dependencies/element-plus.full.min.js
cellbin2/modules/report/js/dependencies/icons-vue.js
cellbin2/modules/report/js/dependencies/jquery-1.10.2.min.js
cellbin2/modules/report/js/dependencies/jquery.dataTables.min.js
cellbin2/modules/report/js/dependencies/panzoom-4.5.1.min.js
cellbin2/modules/report/js/dependencies/plot.js
cellbin2/modules/report/js/dependencies/vue.global.prod.js
cellbin2/modules/report/js/module/Addistribution.js
cellbin2/modules/report/js/module/Cbdistribution.js
cellbin2/modules/report/js/module/CellSeg.js
cellbin2/modules/report/js/module/Cluster.js
cellbin2/modules/report/js/module/CommandLine.js
cellbin2/modules/report/js/module/Common.js
cellbin2/modules/report/js/module/Commonsummary.js
cellbin2/modules/report/js/module/Correlations.js
cellbin2/modules/report/js/module/Counts.js
cellbin2/modules/report/js/module/Distribution.js
cellbin2/modules/report/js/module/Expression.js
cellbin2/modules/report/js/module/ExpressionRightMsg.js
cellbin2/modules/report/js/module/Information.js
cellbin2/modules/report/js/module/KeyMetrics.js
cellbin2/modules/report/js/module/MarkerCluster.js
cellbin2/modules/report/js/module/MarkerTable.js
cellbin2/modules/report/js/module/Microbe.js
cellbin2/modules/report/js/module/Saturation.js
cellbin2/modules/report/js/module/SquareTable.js
cellbin2/modules/report/js/module/Sunburst.js
cellbin2/modules/report/js/module/TissueSeg.js
cellbin2/modules/report/js/module/Title.js
cellbin2/modules/report/js/module/TrackPoint.js
cellbin2/utils/__init__.py
cellbin2/utils/cell_shape.py
cellbin2/utils/clog.py
cellbin2/utils/common.py
cellbin2/utils/config.py
cellbin2/utils/ipr.py
cellbin2/utils/matrix.py
cellbin2/utils/plot_funcs.py
cellbin2/utils/pro_monitor.py
cellbin2/utils/rle.py
cellbin2/utils/rpi.py
cellbin2/utils/stereo.py
cellbin2/utils/stereo_chip.py
cellbin2/utils/stereo_chip_name.py
cellbin2/utils/tar.py
cellbin2/utils/weights_manager.py
docs/v2/update_readme.py
paper/xenium.py
test/demo.py
test/test_cellbin_pipeline.py
test/test_tissue_seg.py
test/utils/test_clog.py
tutorials/mask2geojson.py
tutorials/masks_calc.py
tutorials/test_gpu.py
tutorials/transImage.py