Added

• Hover-Net based digital pathology workflows including new network, loss, postprocessing, metric, training, and inference modules
• Various enhancements for Auto3dSeg AutoRunner including template caching, selection, and a dry-run mode nni_dry_run
• Various enhancements for Auto3dSeg algo templates including new state-of-the-art configurations, optimized GPU memory utilization
• New bundle API and configurations to support experiment management including MLFlowHandler
• New bundle.script API to support model zoo query and download
• LossMetric metric to compute loss as cumulative metric measurement
• Transforms and base transform APIs including RandomizableTrait and MedianSmooth
• runtime_cache option for CacheDataset and the derived classes to allow for shared caching on the fly
• Flexible name formatter for SaveImage transform
• pending_operations MetaTensor property and basic APIs for lazy image resampling
• Contrastive sensitivity for SSIM metric
• Extensible backbones for FlexibleUNet
• Generalize SobelGradients to 3D and any spatial axes
• warmup_multiplier option for WarmupCosineSchedule
• F beta score metric based on confusion matrix metric
• Support of key overwriting in LambdaD
• Basic premerge tests for Python 3.11
• Unit and integration tests for CUDA 11.6, 11.7 and A100 GPU
• DataAnalyzer handles minor image-label shape inconsistencies

Fixed

• Review and enhance previously untyped APIs with additional type annotations and casts
• switch_endianness in LoadImage now supports tensor input
• Reduced memory footprint for various Auto3dSeg tests
• Issue of @ in monai.bundle.ReferenceResolver
• Compatibility issue with ITK-Python 5.3 (converting itkMatrixF44 for default collate)
• Inconsistent of sform and qform when using different backends for SaveImage
• MetaTensor.shape call now returns a torch.Size instead of tuple
• Issue of channel reduction in GeneralizedDiceLoss
• Issue of background handling before softmax in DiceFocalLoss
• Numerical issue of LocalNormalizedCrossCorrelationLoss
• Issue of incompatible view size in ConfusionMatrixMetric
• NetAdapter compatibility with Torchscript
• Issue of extract_levels in RegUNet
• Optional bias_downsample in ResNet
• dtype overflow for ShiftIntensity transform
• Randomized transforms such as RandCuCIM now inherit RandomizableTrait
• fg_indices.size compatibility issue in generate_pos_neg_label_crop_centers
• Issue when inverting ToTensor
• Issue of capital letters in filename suffixes check in LoadImage
• Minor tensor compatibility issues in apps.nuclick.transforms
• Issue of float16 in verify_net_in_out
• std variable type issue for RandRicianNoise
• DataAnalyzer accepts None as label key and checks empty labels
• iter_patch_position now has a smaller memory footprint
• CumulativeAverage has been refactored and enhanced to allow for simple tracking of metric running stats.
• Multi-threading issue for MLFlowHandler

Changed

• Printing a MetaTensor now generates a less verbose representation
• DistributedSampler raises a ValueError if there are too few devices
• OpenCV and VideoDataset modules are loaded lazily to avoid dependency issues
• device in monai.engines.Workflow supports string values
• Activations and AsDiscrete take kwargs as additional arguments
• DataAnalyzer is now more efficient and writes summary stats before detailed all case stats
• Base Docker image upgraded to nvcr.io/nvidia/pytorch:22.10-py3 from nvcr.io/nvidia/pytorch:22.09-py3
• Simplified Conda environment file environment-dev.yml
• Versioneer dependency upgraded to 0.23 from 0.19

Deprecated

• NibabelReader input argument dtype is deprecated, the reader will use the original dtype of the image

Removed

• Support for PyTorch 1.7