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update figures (#5760)
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Signed-off-by: Wenqi Li <[email protected]>

part of #5626


### Types of changes
<!--- Put an `x` in all the boxes that apply, and remove the not
applicable items -->
- [x] Non-breaking change (fix or new feature that would not break
existing functionality).
- [ ] Breaking change (fix or new feature that would cause existing
functionality to change).
- [ ] New tests added to cover the changes.
- [ ] Integration tests passed locally by running `./runtests.sh -f -u
--net --coverage`.
- [ ] Quick tests passed locally by running `./runtests.sh --quick
--unittests --disttests`.
- [ ] In-line docstrings updated.
- [ ] Documentation updated, tested `make html` command in the `docs/`
folder.

Signed-off-by: Wenqi Li <[email protected]>
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wyli authored Dec 18, 2022
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12 changes: 10 additions & 2 deletions docs/source/whatsnew_1_1.md
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Expand Up @@ -8,6 +8,8 @@

## Digital pathology workflows

![hovernet](../images/hovernet_diagram.png)

Hover-Net is a model for simultaneous segmentation and classification of nuclei in multi-tissue histology images (Graham et al. Medical Image Analysis, 2019).
We have added support for this model in MONAI by implementing several new components, enhancing existing ones and providing pipelines and examples for training, validation and inference.

Expand All @@ -22,6 +24,8 @@ and [inference](https://github.com/Project-MONAI/tutorials/blob/main/pathology/n

## Experiment management for MONAI bundle

![exp_mgmt](../images/exp_mgmt.png)

In this release, experiment management features are integrated with MONAI bundle.
It provides essential APIs for managing the end-to-end model bundle lifecycle.
Users can start tracking experiments by, for example, appending `--tracking "mlflow"` to the training or inference commands to enable the MLFlow-based management.
Expand All @@ -38,6 +42,8 @@ CT and PET images of various resolutions and sizes. A tutorial example of
running Auto3DSeg on the HECKTOR22 challenge dataset is available in MONAI
Tutorials. The tutorial is based on [the HECKTOR22 challenge 1st place solution](https://arxiv.org/abs/2209.10809).
- A new improved version of `Segresnet` Algo is now available in `AutoRunner`.
In this version, data caching is more efficient and the preprocessing transforms are more flexible.
The workflow progresses including the timings of steps are written to console output as well as a YAML file.
- Automatic customization and optimization of the model training configuration
can be achieved according to the GPU devices used. The feature
focuses on determining parameters including batch size of model
Expand All @@ -52,8 +58,10 @@ Notably,
- The `mednist_reg` model demonstrates how to build image registration workflows in MONAI bundle
format. The model uses a ResNet and spatial transformer for hand X-ray image registration based on
[the registration_mednist tutorial](https://github.com/Project-MONAI/tutorials/blob/main/2d_registration/registration_mednist.ipynb),
- `pathology_nuclei_segmentation_and_classification`, `pathology_nuclick_annotation`, and
`pathology_nuclei_classification` bundles are built for digital pathology image analysis.
- `pathology_nuclei_segmentation_and_classification`,
`pathology_nuclick_annotation`, and `pathology_nuclei_classification` bundles
are built for [digital pathology image
analysis](https://github.com/Project-MONAI/model-zoo/tree/dev/models/pathology_nuclei_segmentation_classification).

For more details about how to use the models, please see [the tutorials](https://github.com/Project-MONAI/tutorials/tree/main/model_zoo).

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2 changes: 1 addition & 1 deletion monai/bundle/scripts.py
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Expand Up @@ -166,7 +166,7 @@ def _download_from_ngc(download_path: Path, filename: str, version: str, remove_
url = _get_ngc_bundle_url(model_name=filename, version=version)
filepath = download_path / f"{filename}_v{version}.zip"
if remove_prefix:
filename = _remove_ngc_prefix(filename)
filename = _remove_ngc_prefix(filename, prefix=remove_prefix)
extract_path = download_path / f"{filename}"
download_url(url=url, filepath=filepath, hash_val=None, progress=progress)
extractall(filepath=filepath, output_dir=extract_path, has_base=True)
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