spatialproteomics

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Spatialproteomics is a light weight wrapper around xarray with the intention to facilitate the data exploration and analysis of highly multiplexed immunohistochemistry data. Docs available here: https://sagar87.github.io/spatialproteomics/ .

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최종 버전 다운로드 (.zip)

- - branch.yaml
  - release.yaml
- input.tiff
- - style.css
- - layout.html
- - ArtifactRemoval.ipynb
  - CellTypePrediction.ipynb
  - Customizability.ipynb
  - DownstreamAnalysis.ipynb
  - ExampleWorkflow.ipynb
  - ExampleWorkflowSpatialdata.ipynb
  - FAQ.ipynb
  - ImageProcessing.ipynb
  - Installation.ipynb
  - Interactivity.ipynb
  - Interoperability.ipynb
  - MultiTechnologyIntegration.ipynb
  - Neighborhoods.ipynb
  - Plotting.ipynb
  - Segmentation.ipynb
  - Slicing.ipynb
- conf.py
- image_container.rst
- index.rst
- label.rst
- make.bat
- Makefile
- neighborhood.rst
- plot.rst
- preprocessing.rst
- preview.png
- preview2.png
- tool.rst
- - __init__.py
  - ImageContainer.py
- - __init__.py
  - label.py
  - utils.py
- - __init__.py
  - neighborhood.py
  - utils.py
- - __init__.py
  - plot.py
  - utils.py
- - __init__.py
  - intensity.py
  - preprocessing.py
  - utils.py
- - __init__.py
  - utils.py
- - __init__.py
  - tool.py
  - utils.py
- __init__.py
- base_logger.py
- constants.py
- container.py
- - test_image_container.py
- - test_add_label_type.py
  - test_add_labels.py
  - test_format_labels.py
  - test_label_properties.py
  - test_label_select_deselect.py
  - test_predict_cell_subtypes.py
  - test_predict_cell_types_argmax.py
  - test_remove_label_type.py
  - test_set_label_level.py
  - test_threshold_label.py
- - test_add_neighborhood_obs.py
  - test_compute_graph_features.py
  - test_compute_neighborhood_features.py
  - test_compute_neighborhoods_delaunay.py
  - test_compute_neighborhoods_knn.py
  - test_compute_neighborhoods_radius.py
  - test_nh_select_deselect.py
  - test_set_neighborhood_name.py
- - test_colorize.py
  - test_label_segmentation_mask.py
  - test_show.py
- - test_add_channel.py
  - test_add_layer.py
  - test_add_obs.py
  - test_add_quantification.py
  - test_add_segmentation.py
  - test_apply.py
  - test_convert_to_8bit.py
  - test_drop_channel.py
  - test_drop_layers.py
  - test_drop_observations.py
  - test_filter_by_obs.py
  - test_find_bright_cells.py
  - test_get_layer_as_df.py
  - test_grow_cells.py
  - test_handle_disconnected_cells.py
  - test_image_normalize.py
  - test_mask_cells.py
  - test_mask_region.py
  - test_merge_channels.py
  - test_merge_segmentation.py
  - test_remove_outlying_cells.py
  - test_slicing.py
  - test_threshold.py
  - test_threshold_against_snapshot.py
  - test_transform_expression_matrix.py
- - generate_threshold_snapshot.py
- - threshold_snapshots.json
- - test_integration_spatialdata.py
- - image.tiff
  - segmentation.tiff
- - test_cellpose.py
  - test_convert_to_anndata.py
  - test_convert_to_spatialdata.py
- __init__.py
- conftest.py
- test_container.py
- test_integration.py
- test_to_zarr.py
.flake8
.gitignore
CONTRIBUTING.md
LICENSE
Makefile
pyproject.toml
README.md
uv.lock

// repository documentation

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