Baysor

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BAYSOR v0.6.2 ERROR: LoadError: MethodError: no method matching adjacency_list(::Vector{Any}; adjacency_type::Symbol, filter::Bool, return_tesselation::Bool)

4

Dear support, When I tried to run the iss example data (with dapi) using the default config file provided (iss.toml), I ran into this error: ``` baysor run pciSeq_3-3.csv DAPI_3-3_mask.tif...

andynkili

Error when using prior segmentation

1

Hi there, I am trying to use baysor v.0.6.2 and seeing the following error when I try to include a prior segmentation file (tiff format) > [11:01:58] Info: Run R792106752...

kleejin

Hi, I was wondering if it is possible to tweak to Baysor parameters to get a nuclear expansion like approach. Basically, for our dataset, we have an extremely good DAPI...

maximilian-heeg

Hello! Thank you for the tool. I am interested in trying this tool on my own data(Stereo-seq data['geneID', 'x', 'y', 'MIDCounts']). baysor run ./stereo-seq.csv -p -c ./configs/example_config.toml -p -o ./stereo-seq_output_no_dapi/...

mzj0418

Hi, when I run the STARmap example, the following problem occurs baysor preview -x 'x' -y 'y' -g 'gene' -c configs/starmap.toml -o output_dapi molecules.csv [19:16:50] Info: (2023-09-13) Run Baysor v0.6.2...

HongBei-SS

Hi all, I'm running into an error where I get the following warnings: ``` [20:27:11] Info: Initializing algorithm. Scale: 3.5393893702419215, scale std: 0.9835515517434045, initial #components: 1630858, #molecules: 2446289. [20:28:06] Info:...

hchen725

Dear developpers, Thank you for Baysor! I am trying to use it on our merfish data with your merfish.toml config file (github). I use the latest docker version (the one...

andynkili

Container installation / singularity image

1

Given the large memory requirements that Baysor needs to process samples with millions of spots, I wonder if it would be possible to improve the stability of the docker container...

sebgoti

We are trying to integrate Baysor cell segmentation with Merscope downstream analysis tools but we are struggling to get the Baysor output geojson to work with the next steps. It...

PoolLab

Precompilation warnings during Baysor run

1

Hi! Thanks for putting together an awesome package and algorithm. I'm not super familiar with Julia so my apologies if this is something super trivial. I've been running Baysor on...

hchen725