ConstensouxAlexis

Implicit change in matplotlib parameters while importing scimap

3

Hello, I use SCIMAP package with Xenium spatial transcriptomics data. Before importing SCIMAP, I have no issues with plotting the Xenium data:  But, when I import SCIMAP package and...

Using groups in pl.render_shapes() fails with large data

1

Hello, I work with **spatialdata-plot version: 0.2.7.dev2+g6ffe22b** on the following visium HD data:  I have annotated the 8um bins table with cell clusters:  When I do a subset...

Hello, I am trying to compute the AUC score for a custom gene set, on Xenium spatial transcriptomics, with omicverse 1.6.10 Running single.geneset_aucell with default parameters raises "Assertion error: an...

[Question] Assignement of transcripts located on polygons overlap after patch segmentation

1

Hello ! I have a question regarding patches aggregation, after Baysor has been run on several patches. Overlap between patches produces overlapping polygons, that are merged (or not) depending on...

VisiumHD: load scalefactor microns_per_pixel in anndata

5

Hello, Segmentation of nuclei on VisiumHD H&E image might require (at least for StarDist segmentation model) to have the micron per pixel information (since pre trained models can be trained...

Hi, I work with spatialdata 0.3.0, and spatialdata_plot 0.2.9. When calling render_shapes() on Merfish data, with a color argument, plot fails with error: `ValueError: cannot insert EntityID, already exists`. This...

Specify prior segmentation

2

Hello, I have 2 questions regarding the use of nucleus segmentation as prior segmentation: 1. In Merscope data, I do not see any information on nucleus in the detected_transcripts.csv; in...

Xeniumranger import-segmentation producing different cell polygons (less than 4 vertices polygons)

5

Hello, I ran Baysor v0.7, and tried to import the segmentation results with xeniumranger 3.1 import-segmentation. I followed the steps explained in 10x website, and made sure the files format...