Skip to content

demo for 2D slice analysis based on 3D inputs#747

Merged
wyli merged 5 commits intoProject-MONAI:mainfrom
wyli:2d-3d-training
Jun 12, 2022
Merged

demo for 2D slice analysis based on 3D inputs#747
wyli merged 5 commits intoProject-MONAI:mainfrom
wyli:2d-3d-training

Conversation

@wyli
Copy link
Copy Markdown
Contributor

@wyli wyli commented Jun 5, 2022

Signed-off-by: Wenqi Li [email protected]

Fixes #130

  • basic binary seg example with random 2D samples + 2d unet for 3D inputs
  • inference with a sliceinferer

Screenshot 2022-06-05 at 22 07 12

Status

Ready

Checks

  • Notebook runs automatically ./runner [-p <regex_pattern>]

@wyli wyli marked this pull request as ready for review June 5, 2022 22:15
@wyli wyli force-pushed the 2d-3d-training branch from f78a1e5 to 2b320e8 Compare June 5, 2022 23:05
Copy link
Copy Markdown
Contributor

@Nic-Ma Nic-Ma left a comment

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

Hi @wyli ,

Thanks for the quick demo.
Could you please help add more description for the 2 typical methods in this example?
(1) Randomly crop slices for training, (2) Slices for inference.
Or maybe it's better to convert it into a jupyter notebook? So we can include the plot charts of matshow3d or image slices in it?

Thanks.

@wyli
Copy link
Copy Markdown
Contributor Author

wyli commented Jun 6, 2022

thanks, I'll try to convert this script into a notebook example.

wyli added 4 commits June 10, 2022 15:12
Signed-off-by: Wenqi Li <[email protected]>
Signed-off-by: Wenqi Li <[email protected]>
Signed-off-by: Wenqi Li <[email protected]>
@wyli wyli force-pushed the 2d-3d-training branch from b4648a5 to 1dfa20c Compare June 10, 2022 14:31
@review-notebook-app
Copy link
Copy Markdown

Check out this pull request on  ReviewNB

See visual diffs & provide feedback on Jupyter Notebooks.


Powered by ReviewNB

@wyli wyli merged commit c3a7e95 into Project-MONAI:main Jun 12, 2022
@wyli wyli deleted the 2d-3d-training branch June 12, 2022 10:06
@wyli
Copy link
Copy Markdown
Contributor Author

wyli commented Jun 12, 2022

merging these notebooks @Nic-Ma @dannyhow12, please let me know any further questions.

boneseva pushed a commit to boneseva/MONAI-tutorials that referenced this pull request Apr 21, 2024
* adds 2d/3d example

Signed-off-by: Wenqi Li <[email protected]>

* adds eval

Signed-off-by: Wenqi Li <[email protected]>

* update to use EnsureChannelFirstd

Signed-off-by: Wenqi Li <[email protected]>

* update to use notebooks

Signed-off-by: Wenqi Li <[email protected]>

* update to use the weekly build

Signed-off-by: Wenqi Li <[email protected]>
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment

Labels

None yet

Projects

None yet

Development

Successfully merging this pull request may close these issues.

tutorial/demo for 2D slice analysis based on 3D inputs

2 participants