Skip to content

Commit a068209

Browse files
authored
update figures (#5760)
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]>
1 parent 67d84d3 commit a068209

File tree

3 files changed

+11
-3
lines changed

3 files changed

+11
-3
lines changed

docs/images/hovernet_diagram.png

53.8 KB
Loading

docs/source/whatsnew_1_1.md

Lines changed: 10 additions & 2 deletions
Original file line numberDiff line numberDiff line change
@@ -8,6 +8,8 @@
88

99
## Digital pathology workflows
1010

11+
![hovernet](../images/hovernet_diagram.png)
12+
1113
Hover-Net is a model for simultaneous segmentation and classification of nuclei in multi-tissue histology images (Graham et al. Medical Image Analysis, 2019).
1214
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.
1315

@@ -22,6 +24,8 @@ and [inference](https://github.com/Project-MONAI/tutorials/blob/main/pathology/n
2224

2325
## Experiment management for MONAI bundle
2426

27+
![exp_mgmt](../images/exp_mgmt.png)
28+
2529
In this release, experiment management features are integrated with MONAI bundle.
2630
It provides essential APIs for managing the end-to-end model bundle lifecycle.
2731
Users can start tracking experiments by, for example, appending `--tracking "mlflow"` to the training or inference commands to enable the MLFlow-based management.
@@ -38,6 +42,8 @@ CT and PET images of various resolutions and sizes. A tutorial example of
3842
running Auto3DSeg on the HECKTOR22 challenge dataset is available in MONAI
3943
Tutorials. The tutorial is based on [the HECKTOR22 challenge 1st place solution](https://arxiv.org/abs/2209.10809).
4044
- A new improved version of `Segresnet` Algo is now available in `AutoRunner`.
45+
In this version, data caching is more efficient and the preprocessing transforms are more flexible.
46+
The workflow progresses including the timings of steps are written to console output as well as a YAML file.
4147
- Automatic customization and optimization of the model training configuration
4248
can be achieved according to the GPU devices used. The feature
4349
focuses on determining parameters including batch size of model
@@ -52,8 +58,10 @@ Notably,
5258
- The `mednist_reg` model demonstrates how to build image registration workflows in MONAI bundle
5359
format. The model uses a ResNet and spatial transformer for hand X-ray image registration based on
5460
[the registration_mednist tutorial](https://github.com/Project-MONAI/tutorials/blob/main/2d_registration/registration_mednist.ipynb),
55-
- `pathology_nuclei_segmentation_and_classification`, `pathology_nuclick_annotation`, and
56-
`pathology_nuclei_classification` bundles are built for digital pathology image analysis.
61+
- `pathology_nuclei_segmentation_and_classification`,
62+
`pathology_nuclick_annotation`, and `pathology_nuclei_classification` bundles
63+
are built for [digital pathology image
64+
analysis](https://github.com/Project-MONAI/model-zoo/tree/dev/models/pathology_nuclei_segmentation_classification).
5765

5866
For more details about how to use the models, please see [the tutorials](https://github.com/Project-MONAI/tutorials/tree/main/model_zoo).
5967

monai/bundle/scripts.py

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -166,7 +166,7 @@ def _download_from_ngc(download_path: Path, filename: str, version: str, remove_
166166
url = _get_ngc_bundle_url(model_name=filename, version=version)
167167
filepath = download_path / f"{filename}_v{version}.zip"
168168
if remove_prefix:
169-
filename = _remove_ngc_prefix(filename)
169+
filename = _remove_ngc_prefix(filename, prefix=remove_prefix)
170170
extract_path = download_path / f"{filename}"
171171
download_url(url=url, filepath=filepath, hash_val=None, progress=progress)
172172
extractall(filepath=filepath, output_dir=extract_path, has_base=True)

0 commit comments

Comments
 (0)