proseg
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dcjones
Probabilistic cell segmentation for in situ spatial transcriptomics
What are pros and cons of using expected counts from proseg rather than the integer count matrix produced when exporting to 10x format ? Which is recommended for use in...
Hi, Thank you for all your work on Proseg. I ran Proseg2 on Xenium 5K and I have few questions please: I get a warning on the Xenium analysis summary...
Recently, it has been published that monocytes and macrophages fuse to form giant macrophages. Will ProSeg handle it? > HNSCC also contains macrophages that exhibit a large cytoplasm and multiple...
Hi, I have applied proseg to resegment our Xenium data. I plotted the cell patches but it seems some pixels are lost inside of cell polygons (small black dots inside...
Now that there is [public data generated](https://www.10xgenomics.com/datasets/xenium-protein-ffpe-human-renal-carcinoma) by the new RNA and protein Xenium assay, could the diffusion algorithm be benchmarked? It appears more severe than I imagined that it...
Hi @dcjones, I was running the public lymph node 6k dataset with Proseg, and it is taking more than 12 hours and counting. Is this normal? I am using a...
Hey! I'm currently working over an openst spatial data, which is not included over your protocols' list. I saw there is an option running a custom protocol defining the right...
Hi, When using proseg for spaceranger I encountered something I cannot explain: When reading in the visiumHD data, proseg always displays more than twice as much genes as they are...
Hi, first of all thank you for developing such a cool package - particularly now that it is compatible with Visium HD, in my opinion it adresses many caveats of...
Hello! I notice this error initially addressed in #109, but I am not finding the resolution I am looking for. I have six Visium HD samples. They were all run...
