spatialxe
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nf-core
Version `3.5.1` of [nf-core/tools](https://github.com/nf-core/tools) has just been released with updates to the nf-core template. For more details, check out the blog post: https://nf-co.re/blog/2025/tools-3_5_0 Please make sure to merge this pull-request...
### Description of feature Use plotting functions instead of HTML injection into multiqc report
### Description of the bug Attached below is the screenshot of the snap file image based mode should have output paths prefixed with image and not coordinate { "-profile test":...
### Description of feature Baysor fails when the segmentation vector is empty, as it runs the reduce method on an empty vector the error pops up
### Description of feature Be able to read in other image formats (png, jpg) / convert to different data formats (tiff to png, png to zarr, zarr to png)
using spatialdata object input, dynamic segmentation mask detection (cytosol/nucleus), and integrated test case using nf-test and Xenium test data.
#Summary This PR introduces the Points2Regions module for spatial clustering and visualization of transcript data. It includes: - POINTS2REGIONS_CLUSTER: performs clustering using the Points2Regions model. - POINTS2REGIONS_PLOT: visualizes the spatial...
### Description of feature https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10787788/
### Description of feature Create a nextflow module for the [BOMS](https://github.com/ocimakamboj/boms) segmentation tool Scripts: modules/nf-core/boms Refer to : [BOMS - pypi](https://pypi.org/project/boms/)
### Description of feature Translate cell coordinates to pixel coordinates for all given resolutions. You need to calculate scaling factors for this.