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Recent Releases of monailabel

monailabel - 0.8.4

What's New:

  • VISTA2D Dependencies Added:

    • Added dependencies for VISTA2D, ensuring enhanced compatibility and performance when using this feature.

  • Cellprofiler App and Plugin:

    • The Cellprofiler app has been integrated along with a corresponding plugin, enabling new workflows for image analysis.

Enhancements:

  • Release Checks and Updates:

    • Updates and improvements made in preparation for the 0.8.4 release.

  • Allow Newer Versions of Dependencies:

    • Newer versions of key dependencies are now supported, improving compatibility across a wider range of environments.

  • Replace Deprecated IgniteMetric with IgniteMetricHandler:

    • The deprecated IgniteMetric has been replaced with IgniteMetricHandler to keep up with library updates and prevent potential issues.

  • MITK Platform Support:

    • MITK has been officially added as a supported platform, expanding the tool's versatility in medical image processing.

Bug Fixes:

  • Fix Non-Standard English Double-Colons:

    • Addressed issues with non-standard English double colons, ensuring improved consistency in documentation and messaging.

  • Fix Bug with Nuclio Docker Container Directory:

    • Resolved a bug in the Nuclio Docker container that could cause directory-related errors, ensuring smoother execution in Docker environments.

Dependency Updates:

  • Bump requests Library:

    • The requests library was updated from 2.31.0 to 2.32.2, addressing security and bug fixes.

  • Bump urllib3 Library:

    • The urllib3 library was updated from 2.2.1 to 2.2.2 to fix known issues and maintain security compliance.

  • Pre-commit Hooks Update:

    • Updated pre-commit hooks to the latest versions, ensuring consistency in code linting and formatting across the project.

Other Changes:

  • Add Test Case for OpenCV Installation:

    • Introduced a test case to ensure both scenarios are enabled when OpenCV is installed, improving test coverage.

  • Fix cv2 Dependency Issues:

    • Resolved conflicts related to the cv2 library to ensure smooth functionality in different environments.

- Python
Published by tangy5 over 1 year ago

monailabel - 0.8.3

What's Changed

  • Add no scribbles model
  • Mark translatable strings MONAILabel 3D Slicer Extension
  • Bump actions/setup-node
  • Fixing #1601 - missing server URL error when doing inference
  • Updated pydantic version
  • Bump github/codeql-action
  • Bump actions/upload-artifact
  • Bump actions/setup-python
  • Update version with remove requests and requests-toolbelt version limit
  • Adding save label function to xnat datastore
  • Bump actions/cache
  • Bump codecov/codecov-action
  • Update package dependencies
  • Fix response encoding to explicitly use UTF-8 for HTTP response data
  • Update fastapi version
  • update github monai model zoo config
  • Update blossom-ci list
  • Downgraded filelock version
  • Fixed cv2
  • Jwt package for 0.8.2
  • Update bundle versions to avoid conflicts
  • Update more bundle versions

- Python
Published by tangy5 over 1 year ago

monailabel - MONAI Label 0.8.2-rc3

Tag for 0.8.2 rc3

- Python
Published by tangy5 almost 2 years ago

monailabel - MONAI Label 0.8.0

Added

  • OHIF V3

    • DeepEdit and Segmentation Models are supported
    • Deepgrow and Scribbles yet to be supported

  • Option to download DICOM Seg in Inference API

Changed

  • MONAI Core dependency updated to >= 0.13.0
  • Bug Fixes related to DeepEdit model
  • Documentation Fixes

Removed

  • OHIF V2 will be deprecated

- Python
Published by SachidanandAlle over 2 years ago

monailabel - MONAI Label 0.7.1rc1

Added

  • Add a flag to restore label indexed to the ones defined in the config file

- Python
Published by diazandr3s over 2 years ago

monailabel - MONAI Label 0.7.0

Added

  • Multi Users authentication and KeyCloak Integration

    • MONAI Label APIs with Keycloak integration for user authentication and role based access.
    • Login support for 3D Slicer via MONAILabel + KeyClock.

  • Whole Body CT segmentation

    • Segmenting 104 anatomies in 4 seconds!

  • MONAI Bundle Support Improvements

    • Support visualization of bundle config option.
    • Enhancement of monai-zoo access.
    • Support bundle downloading from NGC.
    • Enhacement of multi-gpu training of bundles.

  • New MONAI Label Tutorial Series

    • Quickstart tutorials and installation instructions in notebooks.

  • Documentation enhancements

Changed

  • Updated pretrained models:

    • segmentation
    • deepedit

  • CI/CD and tests

    • blossom CI/CD and pre-merge pipeline enabled.
    • Increased Unit tests coverage to 80%.

Removed

- Python
Published by tangy5 over 2 years ago

monailabel - MONAI Label 0.6.0

Added

  • Pathology Models
  • QuPath Extension: 0.3.1 | Demo
    • User experience enhancements
    • MONAI Label specific Toolbar actions
    • Drag and Drop ROI to run auto-segmentation models
    • Single click to run interaction models (NuClick)
    • Support Next Sample/ROI for Active Learning
  • Experiment Management
  • 3D Slicer: Detection model support in MONAI Bundle App for Radiology use-case
  • Multi-GPU/Multi-Threaded support for Batch Inference

Changed

  • Support latest version of bundles in MONAI Bundle App
  • Upgrade vertebra pipeline
  • MONAI version >= 1.1.0

Removed

  • DeepEdit model for Nuclei segmentation in Pathology

- Python
Published by SachidanandAlle about 3 years ago

monailabel - Pretrained Model Weights

THIS IS NOT A RELEASE PAGE

Download Pretrained model weights (TEST/DEMO purpose only) for the sample apps from here

- Python
Published by SachidanandAlle over 3 years ago

monailabel - MONAI Label 0.5.2

Added

Changed

  • Option to disable DICOM to NIFTI conversion for OHIF usecase
  • Proxy URL fixes for GCP + DICOMWeb support
  • 3D Slicer UI Improvements
  • Fixes for multi label output of segmentation_nuclei model (Pathology)
  • Improvements on MONAI Bundle App
    • support local bundles (pre-downloaded)
    • support customized scripts

Removed

  • Remove option to run ALL Training Tasks in 3D Slicer (Deprecated)

- Python
Published by SachidanandAlle over 3 years ago

monailabel - MONAI Label 0.5.1

Added

  • Endoscopy Sample App
    • Tool Tracking segmentation model | Demo
    • InBody vs OutBody classification model | Demo
    • DeepEdit interaction model
    • CVAT Integration to support automated workflow to run Active Learning Iterations
  • Multi Stage vertebra segmentation in Radiology App

Changed

  • Improving performance for Radiology App
    • Support cache for pre-transforms in case repeated inference for interaction models
    • Support cache for DICOM Web API responses
    • Optimize pre transforms to run GPU for max throughput
    • Fix DICOM Proxy for wado/qido
  • Improvements for Epistemic (v2) active learning strategy
  • Support for MONAI 1.0.0 and above
  • Fixes Scribbles to support MetaTensor

Removed

  • TTA Based active learning strategy is deprecated

- Python
Published by SachidanandAlle over 3 years ago

monailabel - MONAI Label 0.4.2

Added

Changed

  • Support for MONAI 0.9.1

- Python
Published by SachidanandAlle over 3 years ago

monailabel - MONAI Label 0.4.1

Changed

  • Fix MONAI dependency version to 0.9.0

- Python
Published by SachidanandAlle over 3 years ago

monailabel - MONAI Label 0.4.0

Added

  • Pathology Sample App
    • DeepEdit, Segmentation, NuClick models
    • Digital Slide Archive plugin | Demo
    • QuPath plugin | Demo
  • Histogram-based GraphCut and Gaussian Mixture Model (GMM) based methods for scribbles

Changed

  • Support for MONAI (supports 0.9.0 and above)
  • Radiology Sample App (Aggregation of previous radiology models)
    • DeepEdit, Deepgrow, Segmentation, SegmentationSpleen models
  • NrrdWriter for multi-channel arrays
  • 3D Slicer Fixes
    • Support Segmentation Editor and other UI enhancements
    • Improvements for Scribble Interactions
    • Support for .seg.nrrd segmentation files
    • Support to pre-load existing label masks during image fetch/load
  • Static checks using pre-commit ci

Removed

  • SimpleCRF and dependent functions for scribbles

- Python
Published by SachidanandAlle over 3 years ago

monailabel - MONAI Label 0.3.2

Added

  • SSL and multiple worker options while starting MONAI Label server
  • Scribbles support for OHIF Viewer
  • Add Citation page

Changed

  • Support for MONAI (supports 0.8.1 and above)
  • Fix loading pretrained models for TTA and Epistemic Scoring
  • Fix Load MMAR API for deepgrow/segmentation apps
  • Upgrade PIP Dependencies
  • Documentation Fixes

- Python
Published by SachidanandAlle almost 4 years ago

monailabel - MONAI Label 0.3.1

Added

  • Flexible version support for MONAI (supports 0.8.* instead of 0.8.0)

Changed

  • Strict Flag is set to False while loading pretrained models
  • Fix inverse transform for DeepEdit sample app
  • Documentation Fixes

Removed

  • DeepGrow Left-Atrium

- Python
Published by SachidanandAlle about 4 years ago

monailabel - MONAI Label 0.3.0

Added

  • Multi GPU support for training
    • Support for both Windows and Ubuntu
    • Option to customize GPU selection
  • Multi Label support for DeepEdit
    • DynUNET and UNETR
  • Multi Label support for Deepgrow App
    • Annotate multiple organs (spleen, liver, pancreas, unknown etc..)
    • Train Deepgrow 2D/3D models to learn on existing + new labels submitted
  • 3D Slicer plugin
    • Multi Label Interaction
    • UI Enhancements
    • Train/Update specific model
  • Performance Improvements
    • Dataset (Cached, Persistence, SmartCache)
    • ThreadDataloader
    • Early Stopping
  • Strategy Improvements to support Multi User environment
  • Extensibility for Server APIs

Changed

  • Operate histogram likelihood transform in both normalized and unnormalized modes for Scribbles

Removed

  • DeepGrow Left-Atrium

- Python
Published by SachidanandAlle about 4 years ago

monailabel - MONAI Label 0.2.0

Added

  • Support for DICOMWeb connectivity to local/remote PACS
  • Annotations support via OHIF UI enabled in MONAI Label Server
  • Support for native and custom scoring methods to support next image selection strategies
    • Native support for scoring and image selection using Epistemic Uncertainty and Test-time Augmentations (Aleatoric Uncertainty)
  • Custom ScoringMethod and Strategy implementation documentation
  • Scribbles-based annotation support for all sample apps

Changed

  • Previously named generic apps now have default functionality under deepedit, deepgrow and segmentation
  • Updated Modules Overview documentation to include interaction between ScoringMethod and Strategy

Removed

  • All spleen segmentation sample apps (DeepGrow, DeepEdit, auto-segmentation)

- Python
Published by aihsani over 4 years ago

monailabel - MONAI Label 0.1.0

Added

Highlights

  • Framework for developing and deploying MONAI Label Apps to train and infer AI models
  • Compositional & portable APIs for ease of integration in existing workflows
  • Customizable design for varying user expertise
  • 3DSlicer support
  • Support for multi-label auto-segmentation

Sample Apps

  • Template apps to customize the behavior of DeepGrow and DeepEdit
  • Automated segmentation of left atrium, spleen
  • DeepGrow AI annotation of left atrium, spleen
  • DeepEdit AI annotation of left atrium, spleen

- Python
Published by SachidanandAlle over 4 years ago

monailabel - Pretrained model weights and Test Data

THIS IS NOT A RELEASE PAGE

Download Pretrained model weights (TEST/DEMO only) for sample apps from here

- Python
Published by SachidanandAlle over 4 years ago