Added

• Various Auto3DSeg enhancements and integration tests including multi-node multi-GPU optimization, major usability improvements
• TensorRT and ONNX support for monai.bundle API and the relevant models
• nnU-Net V2 integration monai.apps.nnunet
• Binary and categorical metrics and event handlers using MetricsReloaded
• Python module and CLI entry point for bundle workflows in monai.bundle.workflows and monai.fl.client
• Modular patch inference API including PatchInferer, merger, and splitter
• Initial release of lazy resampling including transforms and MetaTensor implementations
• Bridge for ITK Image object and MetaTensor monai.data.itk_torch_bridge
• Sliding window inference memory efficiency optimization including SlidingWindowInfererAdapt
• Generic kernel filtering transforms ImageFiltered and RandImageFiltered
• Trainable bilateral filters and joint bilateral filters
• ClearML stats and image handlers for experiment tracking

misc.

• Utility functions to warn API default value changes (#5738)
• Support of dot notation to access content of ConfigParser (#5813)
• Softmax version to focal loss (#6544)
• FROC metric for N-dimensional (#6528)
• Extend SurfaceDiceMetric for 3D images (#6549)
• A track_meta option for Lambda and derived transforms (#6385)
• CLIP pre-trained text-to-vision embedding (#6282)
• Optional spacing to surface distances calculations (#6144)
• WSIReader read by power and mpp (#6244)
• Support GPU tensor for GridPatch and GridPatchDataset (#6246)
• SomeOf transform composer (#6143)
• GridPatch with both count and threshold filtering (#6055)

Fixed

transforms

• map_classes_to_indices efficiency issue (#6468)
• Adaptive resampling mode based on backends (#6429)
• Improve Compose encapsulation (#6224)
• User-provided FolderLayout in SaveImage and SaveImaged transforms (#6213)
• SpacingD output shape compute stability (#6126)
• No mutate ratio /user inputs croppad (#6127)
• A warn flag to RandCropByLabelClasses (#6121)
• nan to indicate no_channel, split dim singleton (#6090)
• Compatible padding mode (#6076)
• Allow for missing filename_or_obj key (#5980)
• Spacing pixdim in-place change (#5950)
• Add warning in RandHistogramShift (#5877)
• Exclude cuCIM wrappers from get_transform_backends (#5838)

data

• __format__ implementation of MetaTensor (#6523)
• channel_dim in TiffFileWSIReader and CuCIMWSIReader (#6514)
• Prepend "meta" to MetaTensor.__repr__ and MetaTensor.__str__ for easier identification (#6214)
• MetaTensor slicing issue (#5845)
• Default writer flags (#6147)
• WSIReader defaults and tensor conversion (#6058)
• Remove redundant array copy for WSITiffFileReader (#6089)
• Fix unused arg in SlidingPatchWSIDataset (#6047)
• reverse_indexing for PILReader (#6008)
• Use np.linalg for the small affine inverse (#5967)

metrics and losses

• Removing L2-norm in contrastive loss (L2-norm already present in CosSim) (#6550)
• Fixes the SSIM metric (#6250)
• Efficiency issues of Dice metrics (#6412)
• Generalized Dice issue (#5929)
• Unify output tensor devices for multiple metrics (#5924)

networks

• Make RetinaNet throw errors for NaN only when training (#6479)
• Replace deprecated arg in torchvision models (#6401)
• Improves NVFuser import check (#6399)
• Add device in HoVerNetNuclearTypePostProcessing and HoVerNetInstanceMapPostProcessing (#6333)
• Enhance hovernet load pretrained function (#6269)
• Access to the att_mat in self-attention modules (#6493)
• Optional swinunetr-v2 (#6203)
• Add transform to handle empty box as training data for retinanet_detector (#6170)
• GPU utilization of DiNTS network (#6050)
• A pixelshuffle upsample shape mismatch problem (#5982)
• GEGLU activation function for the MLP Block (#5856)
• Constructors for DenseNet derived classes (#5846)
• Flexible interpolation modes in regunet (#5807)

bundle

• Optimized the deepcopy logic in ConfigParser (#6464)
• Improve check and error message of bundle run (#6400)
• Warn or raise ValueError on duplicated key in json/yaml config (#6252)
• Default metadata and logging values for bundle run (#6072)
• pprint head and tail in bundle script (#5969)
• Config parsing issue for substring reference (#5932)
• Fix instantiate for object instantiation with attribute path (#5866)
• Fix _get_latest_bundle_version issue on Windows (#5787)

engines and handlers

• MLflow handler run bug (#6446)
• monai.engine training attribute check (#6132)
• Update StatsHandler logging message (#6051)
• Added callable options for iteration_log and epoch_log in TensorBoard and MLFlow (#5976)
• CheckpointSaver logging error (#6026)
• Callable options for iteration_log and epoch_log in StatsHandler (#5965)

misc.

• Avoid creating cufile.log when import monai (#6106)
• monai._extensions module compatibility with rocm (#6161)
• Issue of repeated UserWarning: "TypedStorage is deprecated" (#6105)
• Use logging config at module level (#5960)
• Add ITK to the list of optional dependencies (#5858)
• RankFilter to skip logging when the rank is not meeting criteria (#6243)
• Various documentation issues

Changed

• Overall more precise and consistent type annotations
• Optionally depend on PyTorch-Ignite v0.4.11 instead of v0.4.10
• Base Docker image upgraded to nvcr.io/nvidia/pytorch:23.03-py3 from nvcr.io/nvidia/pytorch:22.10-py3

Deprecated

• resample=True; resample=False will be the new default in SaveImage
• random_size=True; random_size=False will be the new default for the random cropping transforms
• image_only=False; image_only=True will be the new default in LoadImage
• AddChannel and AsChannelFirst in favor of EnsureChannelFirst

Removed

• Deprecated APIs since v0.9, including WSIReader from monai.apps, NiftiSaver and PNGSaver from monai.data
• Support for PyTorch 1.8
• Support for Python 3.7