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Paper available at https://doi.org/10.1038/s43856-022-00186-5

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TIA Toolbox 1.6.0 Documentation

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TIA Toolbox 1.6.0 Documentation

Readme
Installation
Pre-trained Models
Usage Examples
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- Basic Functionalities
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- Pipelines
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Algorithms
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- IDaRS Theory
Visualization
API Reference
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- read_registry_files
- DuplicateFilter
- annotation
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  - dsl
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  - storage
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- cli
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- data
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  - small_svs
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- enums
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  - GeometryType
- models
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  - architecture
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    - fetch_pretrained_weights
    - get_pretrained_model
    - hovernet
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    - hovernetplus
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      - HoVerNetPlus
    - idars
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      - IDaRS
    - mapde
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      - MapDe
    - micronet
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    - nuclick
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    - sccnn
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      - SCCNN
    - unet
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    - utils
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    - vanilla
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  - dataset
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    - classification
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    - dataset_abc
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      - PatchDatasetABC
    - info
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      - DatasetInfoABC
      - KatherPatchDataset
  - engine
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    - multi_task_segmentor
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      - MultiTaskSegmentor
    - nucleus_instance_segmentor
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      - NucleusInstanceSegmentor
    - patch_predictor
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      - IOPatchPredictorConfig
      - PatchPredictor
    - semantic_segmentor
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  - models_abc
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- tiatoolbox
- tools
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  - graph
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  - patchextraction
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  - pyramid
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  - registration
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    - wsi_registration
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  - stainaugment
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    - StainAugmentor
  - stainextract
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  - stainnorm
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  - tissuemask
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- type_hints
- utils
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  - env_detection
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  - exceptions
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    - tiatoolbox.utils.exceptions.FileNotSupportedError
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  - image
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  - magic
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    - is_dcm
    - is_dir
    - is_sqlite3
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  - metrics
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  - misc
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  - tiff_to_fsspec
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  - transforms
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  - visualization
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- visualization
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  - bokeh_app
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    - app_hooks
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      - on_session_destroyed
    - main
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  - tileserver
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    - TileServer
  - ui_utils
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    - get_level_by_extent
- wsicore
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  - metadata
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    - ngff
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      - Axis
      - Channel
      - CoordinateTransform
      - Creator
      - Dataset
      - Multiscales
      - Omero
      - RDefs
      - Window
      - Zattrs
  - wsimeta
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    - WSIMeta
  - wsireader
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Contributing
Authors
History

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metadata¶

tiatoolbox . wsicore . metadata

Initalizes wsicore.metadata.

Generation of metadata for the OME-NGFF (zarr) slides.

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