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.

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

Example Dataset - Cropped FOV 0 #859

Merged
merged 13 commits into from
Jan 9, 2023
Merged

Conversation

srivarra
Copy link
Contributor

@srivarra srivarra commented Dec 13, 2022

If you haven't already, please read through our contributing guidelines before opening your PR

What is the purpose of this PR?

Closes #817. Converts FOV 0 from a $1024 \times 1024$ image to $512 \times 512$.

How did you implement your changes

  • Added the smaller FOV, reran through all notebooks, zipped up the necessary data files in the HF PR.
  • Added a couple of instances of check_contrast=False in skimage.io.imsave.
  • added a constant in settings.py for EXAMPLE_DATASET_REVISION, defaults to "main", change it to the commit ID to test a different branch.

Remaining issues

Will merge in after HF PR 7, HF PR 9 get merged.

Need to address the pkl formats from Spatial LDA. pkl is unsafe and can allow for arbitrary code to execute when unpacked. Better to use a CSV or ZARR file for later.

@srivarra srivarra added the enhancement New feature or request label Dec 13, 2022
@srivarra srivarra self-assigned this Dec 13, 2022
@srivarra srivarra marked this pull request as ready for review January 9, 2023 20:31
Copy link
Member

@ngreenwald ngreenwald left a comment

Choose a reason for hiding this comment

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

How similar were the individual pixie clusters? Was it pretty easy to match them up to the previous ones, or was there some tweaking needed?

@srivarra
Copy link
Contributor Author

srivarra commented Jan 9, 2023

There was a little bit of tweaking, one of the clusters previously got merged into noise and something else. These are the results with the small FOV.
image

Copy link
Member

@ngreenwald ngreenwald left a comment

Choose a reason for hiding this comment

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

kk, looks good

@srivarra srivarra merged commit c649d5e into main Jan 9, 2023
@srivarra srivarra deleted the example_dataset/cropped_fov0 branch January 9, 2023 21:49
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Labels
enhancement New feature or request
Projects
None yet
Development

Successfully merging this pull request may close these issues.

Add smaller image to huggingface dataset
2 participants