├── .gitignore ├── LICENSE ├── README.md ├── cellbin ├── __init__.py ├── cell_labeling │ ├── GMMCorrectForv03.py │ └── __init__.py ├── cell_segmentation │ ├── README.md │ ├── __init__.py │ ├── seg_utils │ │ ├── __init__.py │ │ ├── cell_infer.py │ │ ├── cell_seg_pipeline.py │ │ ├── dataset.py │ │ ├── find_maxima.py │ │ ├── grade.py │ │ ├── models │ │ │ ├── SE_weight_module.py │ │ │ ├── __init__.py │ │ │ └── epsanet.py │ │ ├── resnet_unet.py │ │ ├── transform.py │ │ └── utils.py │ └── segment.py ├── iqc │ ├── ImageQualityAssessment.py │ ├── QCs.py │ ├── __init__.py │ ├── cellbin_codec.py │ ├── constant.py │ ├── extraInfo.json │ ├── image_reader │ │ └── read │ │ │ ├── __init__.py │ │ │ ├── big_image_reader.py │ │ │ ├── fov_reader.py │ │ │ └── motic_reader.py │ ├── models │ │ ├── ST_TP.cfg │ │ └── ST_TP_v1.1.0_5000_5_7.weights │ ├── qc_util.py │ ├── settings.py │ ├── trackCross_net │ │ ├── README.md │ │ ├── __init__.py │ │ ├── common.py │ │ ├── fov_info.py │ │ ├── fov_json.py │ │ ├── fov_qc │ │ │ ├── __init__.py │ │ │ ├── adjust_image.py │ │ │ ├── cross_detector.py │ │ │ ├── map.py │ │ │ ├── model_config.py │ │ │ ├── shape.py │ │ │ ├── template_match.py │ │ │ ├── track_line.py │ │ │ └── track_qc.py │ │ ├── main.py │ │ └── sold2 │ │ │ ├── __init__.py │ │ │ ├── config │ │ │ └── export_line_features.yaml │ │ │ ├── experiment.py │ │ │ ├── export_line_features.py │ │ │ ├── misc │ │ │ ├── __init__.py │ │ │ ├── geometry_utils.py │ │ │ ├── train_utils.py │ │ │ └── visualize_util.py │ │ │ ├── model │ │ │ ├── __init__.py │ │ │ ├── line_detection.py │ │ │ ├── line_detector.py │ │ │ ├── line_matcher.py │ │ │ ├── line_matching.py │ │ │ ├── loss.py │ │ │ ├── lr_scheduler.py │ │ │ ├── metrics.py │ │ │ ├── model_util.py │ │ │ └── nets │ │ │ │ ├── __init__.py │ │ │ │ ├── backbone.py │ │ │ │ ├── descriptor_decoder.py │ │ │ │ ├── heatmap_decoder.py │ │ │ │ ├── junction_decoder.py │ │ │ │ └── lcnn_hourglass.py │ │ │ ├── train.py │ │ │ └── utils │ │ │ └── line_util.py │ └── utils │ │ ├── __init__.py │ │ ├── common.py │ │ └── fov_json.py ├── registration │ ├── __init__.py │ ├── alignment.py │ └── gene_info.py ├── stitching │ ├── __init__.py │ ├── fov_aligner.py │ ├── global_location.py │ ├── template_reference.py │ └── wsi_stitch.py ├── tissue_segmentation │ ├── __init__.py │ ├── onnx_net.py │ ├── processing.py │ └── tools │ │ ├── __init__.py │ │ ├── deep_watershed.py │ │ ├── preprocessing.py │ │ ├── threshold.py │ │ └── uity.py └── utils │ ├── __init__.py │ ├── big_image_reader.py │ ├── cellbin_codec.py │ ├── common.py │ ├── fov_json.py │ ├── fov_reader.py │ ├── motic_reader.py │ └── util.py ├── docs ├── CellbinStudio_Manual_20221212.pdf ├── StereoCell.png ├── details.md ├── modules.md └── ui.png ├── requirements.txt └── scripts ├── __init__.py ├── filtering.py ├── labeling.py ├── pipeline.py ├── qc.py ├── registration.py ├── segmentation.py ├── stitching.py └── tissue_bin.py /.gitignore: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/STOmics/CellBin/HEAD/.gitignore -------------------------------------------------------------------------------- /LICENSE: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/STOmics/CellBin/HEAD/LICENSE -------------------------------------------------------------------------------- /README.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/STOmics/CellBin/HEAD/README.md -------------------------------------------------------------------------------- /cellbin/__init__.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/STOmics/CellBin/HEAD/cellbin/__init__.py -------------------------------------------------------------------------------- /cellbin/cell_labeling/GMMCorrectForv03.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/STOmics/CellBin/HEAD/cellbin/cell_labeling/GMMCorrectForv03.py -------------------------------------------------------------------------------- /cellbin/cell_labeling/__init__.py: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /cellbin/cell_segmentation/README.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/STOmics/CellBin/HEAD/cellbin/cell_segmentation/README.md -------------------------------------------------------------------------------- /cellbin/cell_segmentation/__init__.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/STOmics/CellBin/HEAD/cellbin/cell_segmentation/__init__.py -------------------------------------------------------------------------------- /cellbin/cell_segmentation/seg_utils/__init__.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/STOmics/CellBin/HEAD/cellbin/cell_segmentation/seg_utils/__init__.py -------------------------------------------------------------------------------- /cellbin/cell_segmentation/seg_utils/cell_infer.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/STOmics/CellBin/HEAD/cellbin/cell_segmentation/seg_utils/cell_infer.py -------------------------------------------------------------------------------- /cellbin/cell_segmentation/seg_utils/cell_seg_pipeline.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/STOmics/CellBin/HEAD/cellbin/cell_segmentation/seg_utils/cell_seg_pipeline.py -------------------------------------------------------------------------------- /cellbin/cell_segmentation/seg_utils/dataset.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/STOmics/CellBin/HEAD/cellbin/cell_segmentation/seg_utils/dataset.py -------------------------------------------------------------------------------- /cellbin/cell_segmentation/seg_utils/find_maxima.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/STOmics/CellBin/HEAD/cellbin/cell_segmentation/seg_utils/find_maxima.py -------------------------------------------------------------------------------- /cellbin/cell_segmentation/seg_utils/grade.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/STOmics/CellBin/HEAD/cellbin/cell_segmentation/seg_utils/grade.py -------------------------------------------------------------------------------- /cellbin/cell_segmentation/seg_utils/models/SE_weight_module.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/STOmics/CellBin/HEAD/cellbin/cell_segmentation/seg_utils/models/SE_weight_module.py -------------------------------------------------------------------------------- /cellbin/cell_segmentation/seg_utils/models/__init__.py: -------------------------------------------------------------------------------- 1 | from .epsanet import * 2 | -------------------------------------------------------------------------------- /cellbin/cell_segmentation/seg_utils/models/epsanet.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/STOmics/CellBin/HEAD/cellbin/cell_segmentation/seg_utils/models/epsanet.py -------------------------------------------------------------------------------- /cellbin/cell_segmentation/seg_utils/resnet_unet.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/STOmics/CellBin/HEAD/cellbin/cell_segmentation/seg_utils/resnet_unet.py -------------------------------------------------------------------------------- /cellbin/cell_segmentation/seg_utils/transform.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/STOmics/CellBin/HEAD/cellbin/cell_segmentation/seg_utils/transform.py -------------------------------------------------------------------------------- /cellbin/cell_segmentation/seg_utils/utils.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/STOmics/CellBin/HEAD/cellbin/cell_segmentation/seg_utils/utils.py -------------------------------------------------------------------------------- /cellbin/cell_segmentation/segment.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/STOmics/CellBin/HEAD/cellbin/cell_segmentation/segment.py -------------------------------------------------------------------------------- /cellbin/iqc/ImageQualityAssessment.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/STOmics/CellBin/HEAD/cellbin/iqc/ImageQualityAssessment.py -------------------------------------------------------------------------------- /cellbin/iqc/QCs.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/STOmics/CellBin/HEAD/cellbin/iqc/QCs.py -------------------------------------------------------------------------------- /cellbin/iqc/__init__.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/STOmics/CellBin/HEAD/cellbin/iqc/__init__.py -------------------------------------------------------------------------------- /cellbin/iqc/cellbin_codec.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/STOmics/CellBin/HEAD/cellbin/iqc/cellbin_codec.py -------------------------------------------------------------------------------- /cellbin/iqc/constant.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/STOmics/CellBin/HEAD/cellbin/iqc/constant.py -------------------------------------------------------------------------------- /cellbin/iqc/extraInfo.json: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/STOmics/CellBin/HEAD/cellbin/iqc/extraInfo.json -------------------------------------------------------------------------------- /cellbin/iqc/image_reader/read/__init__.py: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /cellbin/iqc/image_reader/read/big_image_reader.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/STOmics/CellBin/HEAD/cellbin/iqc/image_reader/read/big_image_reader.py -------------------------------------------------------------------------------- /cellbin/iqc/image_reader/read/fov_reader.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/STOmics/CellBin/HEAD/cellbin/iqc/image_reader/read/fov_reader.py -------------------------------------------------------------------------------- /cellbin/iqc/image_reader/read/motic_reader.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/STOmics/CellBin/HEAD/cellbin/iqc/image_reader/read/motic_reader.py -------------------------------------------------------------------------------- /cellbin/iqc/models/ST_TP.cfg: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/STOmics/CellBin/HEAD/cellbin/iqc/models/ST_TP.cfg -------------------------------------------------------------------------------- /cellbin/iqc/models/ST_TP_v1.1.0_5000_5_7.weights: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/STOmics/CellBin/HEAD/cellbin/iqc/models/ST_TP_v1.1.0_5000_5_7.weights -------------------------------------------------------------------------------- /cellbin/iqc/qc_util.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/STOmics/CellBin/HEAD/cellbin/iqc/qc_util.py -------------------------------------------------------------------------------- /cellbin/iqc/settings.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/STOmics/CellBin/HEAD/cellbin/iqc/settings.py -------------------------------------------------------------------------------- /cellbin/iqc/trackCross_net/README.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/STOmics/CellBin/HEAD/cellbin/iqc/trackCross_net/README.md -------------------------------------------------------------------------------- /cellbin/iqc/trackCross_net/__init__.py: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /cellbin/iqc/trackCross_net/common.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/STOmics/CellBin/HEAD/cellbin/iqc/trackCross_net/common.py -------------------------------------------------------------------------------- /cellbin/iqc/trackCross_net/fov_info.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/STOmics/CellBin/HEAD/cellbin/iqc/trackCross_net/fov_info.py -------------------------------------------------------------------------------- /cellbin/iqc/trackCross_net/fov_json.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/STOmics/CellBin/HEAD/cellbin/iqc/trackCross_net/fov_json.py -------------------------------------------------------------------------------- /cellbin/iqc/trackCross_net/fov_qc/__init__.py: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /cellbin/iqc/trackCross_net/fov_qc/adjust_image.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/STOmics/CellBin/HEAD/cellbin/iqc/trackCross_net/fov_qc/adjust_image.py -------------------------------------------------------------------------------- /cellbin/iqc/trackCross_net/fov_qc/cross_detector.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/STOmics/CellBin/HEAD/cellbin/iqc/trackCross_net/fov_qc/cross_detector.py -------------------------------------------------------------------------------- /cellbin/iqc/trackCross_net/fov_qc/map.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/STOmics/CellBin/HEAD/cellbin/iqc/trackCross_net/fov_qc/map.py -------------------------------------------------------------------------------- /cellbin/iqc/trackCross_net/fov_qc/model_config.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/STOmics/CellBin/HEAD/cellbin/iqc/trackCross_net/fov_qc/model_config.py -------------------------------------------------------------------------------- /cellbin/iqc/trackCross_net/fov_qc/shape.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/STOmics/CellBin/HEAD/cellbin/iqc/trackCross_net/fov_qc/shape.py -------------------------------------------------------------------------------- /cellbin/iqc/trackCross_net/fov_qc/template_match.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/STOmics/CellBin/HEAD/cellbin/iqc/trackCross_net/fov_qc/template_match.py -------------------------------------------------------------------------------- /cellbin/iqc/trackCross_net/fov_qc/track_line.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/STOmics/CellBin/HEAD/cellbin/iqc/trackCross_net/fov_qc/track_line.py -------------------------------------------------------------------------------- /cellbin/iqc/trackCross_net/fov_qc/track_qc.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/STOmics/CellBin/HEAD/cellbin/iqc/trackCross_net/fov_qc/track_qc.py -------------------------------------------------------------------------------- /cellbin/iqc/trackCross_net/main.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/STOmics/CellBin/HEAD/cellbin/iqc/trackCross_net/main.py -------------------------------------------------------------------------------- /cellbin/iqc/trackCross_net/sold2/__init__.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/STOmics/CellBin/HEAD/cellbin/iqc/trackCross_net/sold2/__init__.py -------------------------------------------------------------------------------- /cellbin/iqc/trackCross_net/sold2/config/export_line_features.yaml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/STOmics/CellBin/HEAD/cellbin/iqc/trackCross_net/sold2/config/export_line_features.yaml -------------------------------------------------------------------------------- /cellbin/iqc/trackCross_net/sold2/experiment.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/STOmics/CellBin/HEAD/cellbin/iqc/trackCross_net/sold2/experiment.py -------------------------------------------------------------------------------- /cellbin/iqc/trackCross_net/sold2/export_line_features.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/STOmics/CellBin/HEAD/cellbin/iqc/trackCross_net/sold2/export_line_features.py -------------------------------------------------------------------------------- /cellbin/iqc/trackCross_net/sold2/misc/__init__.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/STOmics/CellBin/HEAD/cellbin/iqc/trackCross_net/sold2/misc/__init__.py -------------------------------------------------------------------------------- /cellbin/iqc/trackCross_net/sold2/misc/geometry_utils.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/STOmics/CellBin/HEAD/cellbin/iqc/trackCross_net/sold2/misc/geometry_utils.py -------------------------------------------------------------------------------- /cellbin/iqc/trackCross_net/sold2/misc/train_utils.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/STOmics/CellBin/HEAD/cellbin/iqc/trackCross_net/sold2/misc/train_utils.py -------------------------------------------------------------------------------- /cellbin/iqc/trackCross_net/sold2/misc/visualize_util.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/STOmics/CellBin/HEAD/cellbin/iqc/trackCross_net/sold2/misc/visualize_util.py -------------------------------------------------------------------------------- /cellbin/iqc/trackCross_net/sold2/model/__init__.py: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /cellbin/iqc/trackCross_net/sold2/model/line_detection.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/STOmics/CellBin/HEAD/cellbin/iqc/trackCross_net/sold2/model/line_detection.py -------------------------------------------------------------------------------- /cellbin/iqc/trackCross_net/sold2/model/line_detector.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/STOmics/CellBin/HEAD/cellbin/iqc/trackCross_net/sold2/model/line_detector.py -------------------------------------------------------------------------------- /cellbin/iqc/trackCross_net/sold2/model/line_matcher.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/STOmics/CellBin/HEAD/cellbin/iqc/trackCross_net/sold2/model/line_matcher.py -------------------------------------------------------------------------------- /cellbin/iqc/trackCross_net/sold2/model/line_matching.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/STOmics/CellBin/HEAD/cellbin/iqc/trackCross_net/sold2/model/line_matching.py -------------------------------------------------------------------------------- /cellbin/iqc/trackCross_net/sold2/model/loss.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/STOmics/CellBin/HEAD/cellbin/iqc/trackCross_net/sold2/model/loss.py -------------------------------------------------------------------------------- /cellbin/iqc/trackCross_net/sold2/model/lr_scheduler.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/STOmics/CellBin/HEAD/cellbin/iqc/trackCross_net/sold2/model/lr_scheduler.py -------------------------------------------------------------------------------- /cellbin/iqc/trackCross_net/sold2/model/metrics.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/STOmics/CellBin/HEAD/cellbin/iqc/trackCross_net/sold2/model/metrics.py -------------------------------------------------------------------------------- /cellbin/iqc/trackCross_net/sold2/model/model_util.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/STOmics/CellBin/HEAD/cellbin/iqc/trackCross_net/sold2/model/model_util.py -------------------------------------------------------------------------------- /cellbin/iqc/trackCross_net/sold2/model/nets/__init__.py: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /cellbin/iqc/trackCross_net/sold2/model/nets/backbone.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/STOmics/CellBin/HEAD/cellbin/iqc/trackCross_net/sold2/model/nets/backbone.py -------------------------------------------------------------------------------- /cellbin/iqc/trackCross_net/sold2/model/nets/descriptor_decoder.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/STOmics/CellBin/HEAD/cellbin/iqc/trackCross_net/sold2/model/nets/descriptor_decoder.py -------------------------------------------------------------------------------- /cellbin/iqc/trackCross_net/sold2/model/nets/heatmap_decoder.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/STOmics/CellBin/HEAD/cellbin/iqc/trackCross_net/sold2/model/nets/heatmap_decoder.py -------------------------------------------------------------------------------- /cellbin/iqc/trackCross_net/sold2/model/nets/junction_decoder.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/STOmics/CellBin/HEAD/cellbin/iqc/trackCross_net/sold2/model/nets/junction_decoder.py -------------------------------------------------------------------------------- /cellbin/iqc/trackCross_net/sold2/model/nets/lcnn_hourglass.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/STOmics/CellBin/HEAD/cellbin/iqc/trackCross_net/sold2/model/nets/lcnn_hourglass.py -------------------------------------------------------------------------------- /cellbin/iqc/trackCross_net/sold2/train.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/STOmics/CellBin/HEAD/cellbin/iqc/trackCross_net/sold2/train.py -------------------------------------------------------------------------------- /cellbin/iqc/trackCross_net/sold2/utils/line_util.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/STOmics/CellBin/HEAD/cellbin/iqc/trackCross_net/sold2/utils/line_util.py -------------------------------------------------------------------------------- /cellbin/iqc/utils/__init__.py: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /cellbin/iqc/utils/common.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/STOmics/CellBin/HEAD/cellbin/iqc/utils/common.py -------------------------------------------------------------------------------- /cellbin/iqc/utils/fov_json.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/STOmics/CellBin/HEAD/cellbin/iqc/utils/fov_json.py -------------------------------------------------------------------------------- /cellbin/registration/__init__.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/STOmics/CellBin/HEAD/cellbin/registration/__init__.py -------------------------------------------------------------------------------- /cellbin/registration/alignment.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/STOmics/CellBin/HEAD/cellbin/registration/alignment.py -------------------------------------------------------------------------------- /cellbin/registration/gene_info.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/STOmics/CellBin/HEAD/cellbin/registration/gene_info.py -------------------------------------------------------------------------------- /cellbin/stitching/__init__.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/STOmics/CellBin/HEAD/cellbin/stitching/__init__.py -------------------------------------------------------------------------------- /cellbin/stitching/fov_aligner.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/STOmics/CellBin/HEAD/cellbin/stitching/fov_aligner.py -------------------------------------------------------------------------------- /cellbin/stitching/global_location.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/STOmics/CellBin/HEAD/cellbin/stitching/global_location.py -------------------------------------------------------------------------------- /cellbin/stitching/template_reference.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/STOmics/CellBin/HEAD/cellbin/stitching/template_reference.py -------------------------------------------------------------------------------- /cellbin/stitching/wsi_stitch.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/STOmics/CellBin/HEAD/cellbin/stitching/wsi_stitch.py -------------------------------------------------------------------------------- /cellbin/tissue_segmentation/__init__.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/STOmics/CellBin/HEAD/cellbin/tissue_segmentation/__init__.py -------------------------------------------------------------------------------- /cellbin/tissue_segmentation/onnx_net.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/STOmics/CellBin/HEAD/cellbin/tissue_segmentation/onnx_net.py -------------------------------------------------------------------------------- /cellbin/tissue_segmentation/processing.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/STOmics/CellBin/HEAD/cellbin/tissue_segmentation/processing.py -------------------------------------------------------------------------------- /cellbin/tissue_segmentation/tools/__init__.py: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /cellbin/tissue_segmentation/tools/deep_watershed.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/STOmics/CellBin/HEAD/cellbin/tissue_segmentation/tools/deep_watershed.py -------------------------------------------------------------------------------- /cellbin/tissue_segmentation/tools/preprocessing.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/STOmics/CellBin/HEAD/cellbin/tissue_segmentation/tools/preprocessing.py -------------------------------------------------------------------------------- /cellbin/tissue_segmentation/tools/threshold.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/STOmics/CellBin/HEAD/cellbin/tissue_segmentation/tools/threshold.py -------------------------------------------------------------------------------- /cellbin/tissue_segmentation/tools/uity.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/STOmics/CellBin/HEAD/cellbin/tissue_segmentation/tools/uity.py -------------------------------------------------------------------------------- /cellbin/utils/__init__.py: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /cellbin/utils/big_image_reader.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/STOmics/CellBin/HEAD/cellbin/utils/big_image_reader.py -------------------------------------------------------------------------------- /cellbin/utils/cellbin_codec.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/STOmics/CellBin/HEAD/cellbin/utils/cellbin_codec.py -------------------------------------------------------------------------------- /cellbin/utils/common.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/STOmics/CellBin/HEAD/cellbin/utils/common.py -------------------------------------------------------------------------------- /cellbin/utils/fov_json.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/STOmics/CellBin/HEAD/cellbin/utils/fov_json.py -------------------------------------------------------------------------------- /cellbin/utils/fov_reader.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/STOmics/CellBin/HEAD/cellbin/utils/fov_reader.py -------------------------------------------------------------------------------- /cellbin/utils/motic_reader.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/STOmics/CellBin/HEAD/cellbin/utils/motic_reader.py -------------------------------------------------------------------------------- /cellbin/utils/util.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/STOmics/CellBin/HEAD/cellbin/utils/util.py -------------------------------------------------------------------------------- /docs/CellbinStudio_Manual_20221212.pdf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/STOmics/CellBin/HEAD/docs/CellbinStudio_Manual_20221212.pdf -------------------------------------------------------------------------------- /docs/StereoCell.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/STOmics/CellBin/HEAD/docs/StereoCell.png -------------------------------------------------------------------------------- /docs/details.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/STOmics/CellBin/HEAD/docs/details.md -------------------------------------------------------------------------------- /docs/modules.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/STOmics/CellBin/HEAD/docs/modules.md -------------------------------------------------------------------------------- /docs/ui.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/STOmics/CellBin/HEAD/docs/ui.png -------------------------------------------------------------------------------- /requirements.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/STOmics/CellBin/HEAD/requirements.txt -------------------------------------------------------------------------------- /scripts/__init__.py: -------------------------------------------------------------------------------- 1 | 2 | -------------------------------------------------------------------------------- /scripts/filtering.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/STOmics/CellBin/HEAD/scripts/filtering.py -------------------------------------------------------------------------------- /scripts/labeling.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/STOmics/CellBin/HEAD/scripts/labeling.py -------------------------------------------------------------------------------- /scripts/pipeline.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/STOmics/CellBin/HEAD/scripts/pipeline.py -------------------------------------------------------------------------------- /scripts/qc.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/STOmics/CellBin/HEAD/scripts/qc.py -------------------------------------------------------------------------------- /scripts/registration.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/STOmics/CellBin/HEAD/scripts/registration.py -------------------------------------------------------------------------------- /scripts/segmentation.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/STOmics/CellBin/HEAD/scripts/segmentation.py -------------------------------------------------------------------------------- /scripts/stitching.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/STOmics/CellBin/HEAD/scripts/stitching.py -------------------------------------------------------------------------------- /scripts/tissue_bin.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/STOmics/CellBin/HEAD/scripts/tissue_bin.py --------------------------------------------------------------------------------