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

Speckles images issues within example notebook #32

Open
d33bs opened this issue Nov 13, 2024 · 0 comments
Open

Speckles images issues within example notebook #32

d33bs opened this issue Nov 13, 2024 · 0 comments
Labels
bug Something isn't working

Comments

@d33bs
Copy link
Member

d33bs commented Nov 13, 2024

Discussing with @jenna-tomkinson, the example notebook should be updated for the nuclear speckles dataset to only display filename columns which can display images from the testing dataset.

E.g.

%%time
# view nuclear speckles data with images and overlaid outlines from masks
CytoDataFrame(
    data=f"{nuclear_speckles_path}/test_slide1_converted.parquet",
    data_context_dir=f"{nuclear_speckles_path}/images/plate1",
    data_mask_context_dir=f"{nuclear_speckles_path}/masks/plate1",
)[
    [
        "Metadata_ImageNumber",
        "Nuclei_Number_Object_Number",
        "Image_FileName_A647",
        "Image_FileName_DAPI",
        "Image_FileName_GOLD",
    ]
][:3]

To:

%%time
# view nuclear speckles data with images and overlaid outlines from masks
CytoDataFrame(
    data=f"{nuclear_speckles_path}/test_slide1_converted.parquet",
    data_context_dir=f"{nuclear_speckles_path}/images/plate1",
    data_mask_context_dir=f"{nuclear_speckles_path}/masks/plate1",
)[
    [
        "Metadata_ImageNumber",
        "Nuclei_Number_Object_Number",
        "Image_FileName_DAPI",
    ]
][:3]
@d33bs d33bs added the bug Something isn't working label Nov 13, 2024
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Labels
bug Something isn't working
Projects
None yet
Development

No branches or pull requests

1 participant