Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Jump to bottom

Vista-2D Tutorial #1788

Closed
wants to merge 10 commits into from
Closed

Vista-2D Tutorial #1788

wants to merge 10 commits into from

Conversation

finalelement
Copy link
Contributor

Creating a tutorial and dataset preparation resource for Vista-2D from MONAI bundles

Description

Vista-2D Cell Segmentation foundation model with dataset preparation resources as well.

Checks

  • Avoid including large-size files in the PR.
  • Clean up long text outputs from code cells in the notebook.
  • For security purposes, please check the contents and remove any sensitive info such as user names and private key.
  • Ensure (1) hyperlinks and markdown anchors are working (2) use relative paths for tutorial repo files (3) put figure and graphs in the ./figure folder
  • Notebook runs automatically ./runner.sh -t <path to .ipynb file>

@finalelement
First Draft
d01158e 
Signed-off-by: Vishwesh Nath <[email protected]>
@finalelement finalelement marked this pull request as ready for review August 23, 2024 20:41
@finalelement
Jupyter notebook for vista 2D
b812d59 
Signed-off-by: Vishwesh Nath <[email protected]>
@review-notebook-app Review Notebook App
Copy link

Check out this pull request on  ReviewNB

See visual diffs & provide feedback on Jupyter Notebooks.

Powered by ReviewNB

@finalelement
Copy link
Contributor Author

@Nic-Ma I've prepped the first draft of the notebook, there is some more polishing required by my side (like segmentation plots), but overall I think it's almost there for an early review from you.

@finalelement
Notebook prepped
025c85c 
Signed-off-by: Vishwesh Nath <[email protected]>
@finalelement
Copy link
Contributor Author

@Nic-Ma the notebook was further updated with some enhancements for training curve visualization and prediction segmentation plots etc.

KumoLiu
KumoLiu reviewed Sep 3, 2024
View reviewed changes
Copy link
Contributor

@KumoLiu KumoLiu left a comment

Choose a reason for hiding this comment

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

Thanks for the PR! Leave several comments in line.

vista_2d/cell_sam_wrapper.py Outdated Show resolved Hide resolved
vista_2d/cell_sam_wrapper.py Outdated Show resolved Hide resolved
vista_2d/cellpose_datalist.json Outdated Show resolved Hide resolved
vista_2d/cellpose_toy_datalist.json Outdated Show resolved Hide resolved
vista_2d/components.py Outdated Show resolved Hide resolved
vista_2d/components.py Outdated Show resolved Hide resolved
KumoLiu
KumoLiu reviewed Sep 3, 2024
View reviewed changes
vista_2d/vista_2d_tutorial_monai.ipynb
"\n",
"# VISTA-2D Cell Segmentation with Segment Anything Model (SAM) & MONAI\n",
"\n",
"![image](../figures/vista_2d_overview.png)\n",
Copy link
Contributor

Choose a reason for hiding this comment

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

Looks like missing this png here?

Copy link
Contributor Author

Choose a reason for hiding this comment

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

Its added now, it's because, figures need to be specifically added by a -f

@KumoLiu
Copy link
Contributor

KumoLiu commented Sep 3, 2024

Hi @finalelement, could you please help create a new folder named "vista2d" under https://github.com/Project-MONAI/tutorials/tree/main/2d_segmentation? Then move this file into that folder?
cc @Nic-Ma

KumoLiu
KumoLiu reviewed Sep 3, 2024
View reviewed changes
vista_2d/components.py Outdated Show resolved Hide resolved
vista_2d/components.py Show resolved Hide resolved
vista_2d/components.py Outdated Show resolved Hide resolved
KumoLiu
KumoLiu reviewed Sep 3, 2024
View reviewed changes
vista_2d/vista_2d_tutorial_monai.ipynb Show resolved Hide resolved
vista_2d/vista_2d_tutorial_monai.ipynb Show resolved Hide resolved
vista_2d/vista_2d_tutorial_monai.ipynb Show resolved Hide resolved
vista_2d/vista_2d_tutorial_monai.ipynb
@@ -0,0 +1,1405 @@
{
Copy link
Contributor

@KumoLiu KumoLiu Sep 3, 2024 •
edited
Loading

Choose a reason for hiding this comment

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

Could you please help remove the output for this cell? But include the graph in the next cell outout, thanks!


Reply via ReviewNB

Copy link
Contributor Author

Choose a reason for hiding this comment

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

Sure, let me fix it with the next run.

Copy link
Contributor Author

Choose a reason for hiding this comment

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

Sure.

vista_2d/vista_2d_tutorial_monai.ipynb Show resolved Hide resolved
vista_2d/vista_2d_tutorial_monai.ipynb Show resolved Hide resolved
@finalelement
Addressing comments
948af6c 
Signed-off-by: Vishwesh Nath <[email protected]>
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Reviewers

@yiheng-wang-nv yiheng-wang-nv yiheng-wang-nv left review comments

@KumoLiu KumoLiu KumoLiu left review comments

@Nic-Ma Nic-Ma Nic-Ma left review comments

@ericspod ericspod Awaiting requested review from ericspod

@mingxin-zheng mingxin-zheng Awaiting requested review from mingxin-zheng

Assignees
No one assigned
Labels
None yet
Projects
None yet
Milestone
No milestone
Development

Successfully merging this pull request may close these issues.
4 participants
@finalelement @KumoLiu @Nic-Ma @yiheng-wang-nv