Baysor

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ERROR: ArgumentError: Package CSVFiles

2

Hi, I installed Baysor on Linux as a binary and tried to run it on your example data (mRNA_coords_raw_counting.csv) with and without DAPI. But the problem is that I keep...

Dana162001

LoadError: pca must have at least 3 components

1

Hello developers, Many thanks for creating Baysor for spatial transcriptomics field. I am using baysor for 2d cell segmentation for smFISH data for just few handful of genes. I get...

ankitbioinfo

Error: MethodError(Matrix{<:Unsigned}

3

I am apply Baysor to Resolve data. The "preview" step works, and outputs the HTML report, which looks fine, but the "run" step crashes with the following error. Any idea...

ccbvib

Hi Kharchenko lab, I've been trying to implement Baysor on my CosMx data. I wanted some clarification about what Baysor does to overlapping regions. From my understanding of your paper,...

Jwong684

Loading binary image sementation mask as prior: MethodError: no method matching sparse

1

Hi, First of all, thanks for making Baysor, its amazing! Baysor works for me without prior segmentation, but when I add a binary image with a segmentation mask (Black background,...

Sengels24

create a squidpy or R object using baysor output

1

Hi, I want to use baysor segmentation on my CosMx data and then visualize it in R/Python. CosMx usually outputs 5 files which are used by Seurat/Squidpy to create the...

shrutikhare-git

Dear all, Is it possible to get the output of 'clustering molecules' step without proceeding to the segmentation and creating polygons? Thank you, Araks

araksm

Square root of negative value error during "using 3D coordinates"

1

Ran into this error on Xenium data. Had to preprocess Xenium data extensively to get it to be compatible with Baysor, but still throwing an error. Seems to be related...

sapiomr

I just ran Baysor v6.2.0 wit the flag ```--count-matrix-format tsv```. In my output however, the genes are listed as the columns, but the matrix columns exceed the number of gene...

Hannah-Doerpholz

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...

MOSAIFENG