proseg
proseg copied to clipboard
dcjones
Probabilistic cell segmentation for in situ spatial transcriptomics
Hello, I was running Proseg v2.0.1 on my Xenium 5k data. For one sample, I encountered out-of-memory error. I've given 257GB memory for the process already, and rerun with 300GB...
Thank you so much for developing this wonderful tool. I wanted more layers of voxel in proseg segmentation and ran with `--voxel-layers 10` option. The Run program is shown below....
as i understand it from [this page](https://www.10xgenomics.com/support/software/xenium-ranger/2.0/tutorials/running-pipelines/XR-import-segmentation), running xeniumranger --import-segmentation with baysor-style inputs does not generate masks in cells.zarr.zip. yet i would like to use proseg segmentation as a mask...
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...
Hi, Thank you for developing this tool! I'm using it for the segmentation of Xenium data, followed by classical single-cell analysis. However, I've noticed that the expected counts from Proseg...
Hi, Thank you for your time and effort for building proseg. I am facing issues with proseg segmenting some huge cells for my xenium data. Also, does the volume parameter...
Hi @dcjones , Just wondering if you have tested/compared, whether using 3D polygons (3D segmentation) is better than using the 2D projection version for downstream analysis. Thanks, RL
Hi, I was wondering if you have ever tested how the number of iterations set through the --schedule parameter might affect the final proseg output. I noticed that on my...
How does it do on [the classic breast cancer Xenium](https://www.nature.com/articles/s41467-023-43458-x) sample for myoepithelial cells, which have markers of two cell types? > myoepithelial cells demonstrate intermediate expression of tumor cell...
Hi, I installed proseg withouth problems two weeks ago but this weekend I ran into a problem with compiling. Seems like there may be a problem with chrono package? --------------------------------------------------------------------...
