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kharchenkolab / Baysor

Bayesian Segmentation of Spatial Transcriptomics Data
https://kharchenkolab.github.io/Baysor/
MIT License
152 stars 31 forks source link

The HTML file output by the baysor preview or baysor run command exceeds 1 GB, making it impossible to browse using a standard web browser. #121

Closed MOSAIFENG closed 3 weeks ago

MOSAIFENG commented 4 months ago

I used the vpetukhov/baysor.6.2 Docker image of Baysor to re-segment Xenium data. The resulting HTML file exceeds 1 GB, which means it can only be viewed as text using the file editor EmEditor, and cannot be rendered by mainstream browsers.

VPetukhov commented 2 months ago

Yeah, showing whole data for the modern protocols with large tissues is problematic. You can try reducing min_pixels_per_cell in the config. But in general I'd suggest to omit plotting it in the report and doing some manual visualizations.

VPetukhov commented 3 weeks ago

The new version (0.7.0) should have it fixed. Now it's controlled through max_plot_size parameter Please, see the changelog for more details.