Baysor

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About Multithreading / Parallelization

13

Hello! Thank you very much for open-sourcing Baysor! This will help the scientific community for years to come. I was running Baysor in our inhouse datasets and found that it...

arundasan91

Hi @VPetukhov , I'd like to know some information about the cell clustering of Baysor: 1. Are the cells clustered according to their transcriptomic composition? 2. Can we adjust the...

rocketeer1998

Error when estimating boundaries

2

Hi there, I have tried running this on CentOS and MacOS and both instances, the run fails to estimate boundaries and I get the following error. The run still completes...

kleejin

Issue with MacOS binaries

3

Hello, I am having trouble using the MacOS binaries, getting the following message. Any ideas? ./baysor --help Two passes with the same argument (-LowerPTLS) attempted to be registered! zsh: illegal...

kleejin

inconsistent number of cells between the output files

3

The number of cell boundaries in `segmentation_polygons.json` far exceeds the number of cells in `segmentation.csv` and `segmentation_cell_stats.csv`. For example one of my runs produced 4013 polygons but only 2430 cells....

MobiTobi

Errors about boundary_polygons

2

Hi, I'm using the Julia-1.7.0 on ubuntu and successfully ran the Baysor for the first few steps. However, when I want to analyze the boundary using the following codes: grid_step...

JuanruMaryGuo

Prior segmentation doesn't work for not 16-bit tiffs

3

Hi authors, I am trying to run Baysor with a segmentation tif file where the background is 0, and all the indivudual cells are marked with 1,2,3,4...I noticed that Baysor...

YubinXie

Hi Viktor This looks like such a great package, thank you very much for it. I tried using it on my own data while supplying prior segmentation from a DAPI...

GMaciag

Hi, While running the examples from [here](https://github.com/kharchenkolab/BaysorAnalysis/blob/master/notebooks/segmentation_free/segmentation_free_allen_smfish.ipynb) , the execution of ``` sample_ids = Baysor.select_ids_uniformly(df_spatial.x, df_spatial.y, df_spatial.confidence,n= 2000) ``` gives the following error, ``` MethodError: no method matching select_ids_uniformly(::Vector{Int64}, ::Vector{Int64},...

hiraksarkar

Error from `plot_molecules` function

2

Hi, Related to the previous issue, I am trying to build `segmentation_free_allen_smfish` notebook and met with the following error after executing `plot_molecules` ``` sub_lims = [((11000, 13000), (12000, 13500)), ((11500,...

hiraksarkar