pakiessling

map_cells_to_space "could not determine the shape of object type 'Series'" error

3

Hi I am on scanpy=1.9.3 squidpy=1.2.3 tangram=1.0.4 torch=1.13.1+cu117 I am trying to integrate single cell and merfish data. A marker list of 104 genes was correctly prepared and I have...

Support for 10x FFPE scRNA

3

### Description of feature Hi, unsure if this is supported yet. 10x offers new kits to process scRNA from FFPE https://www.10xgenomics.com/products/single-cell-gene-expression-flex The data is processed with `cellranger multi` https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/using/multi It...

Hi there, I am working on creating a converter from Baysor output and I notice that a small percentage of Baysor .geojson output contains less than 4 coordinates and is...

Feature request: Support for 10x "flex" fixed RNA data

3

Hi, 10x has a newish product ["flex"](https://www.10xgenomics.com/products/single-cell-gene-expression-flex) that allows for the sequencing of fixed nuclei. It works based on [a set of 20 000 probes that bind transcripts](https://www.10xgenomics.com/support/single-cell-gene-expression-flex/documentation/steps/probe-sets/chromium-frp-probe-sets-overview) and are...

Converting from .h5Seurat to h5ad messes up observational metadata

1

`SeuratDisk_0.0.0.9019 SeuratData_0.2.2 sp_1.5-0 SeuratObject_4.1.0 Seurat_4.1.1 ` I convert a rds to h5seurat and then h5ad. I encountered the same problem on multiple datasets. Before:  After:  The annotation column...

Hi, If you select multiple different regions on a Merscope you get multiple different folders as output. I am trying to combine them into a single object like this: ```...

Analyzing metadata varying across cells of a donor

4

Hi, thank you for the nice tool. I was wondering how I could apply this tool to my research. I have scRNA samples of different donors. For every donor cells...

3D support

20

Thank you for the tool, I am interested in trying it out. Is it possible to run the algorithm on 3D data such as the 7 z-levels a Merscope outputs?...

Error 404: Not found

6

Hi, thank you for this tool, I am very excited to try it out. Unfortunately, my Slideshow is permanently stuck at 404: Not found. Server log says: ``` 404 GET...

Hi, I want to load VisiumHD data in a pipeline without any images, is there a way to accomplish this?