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Hi, thanks a lot for developing this software. I've been struggling with cell segmentation in 3D for a long time and your software is working so well after training the model with a few images.
I a…
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# Image Alignment
Image alignment in starfish is driven by the need to carry out two tasks:
1. Identify the cell of origin for each spot
2. Identify mRNA molecules whose identity is encoded across…
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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 the followi…
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Hi, scanpy team!
I am trying to understand if `scanpy.pl.spatial` would support using the fullres histology image. E.i. if it supports `img_key = 'fullres` where it would pull the image from 'fullr…
vitkl updated
3 years ago
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Hello, this is an excellent piece of work. Based on the code provided in the "MERFISH_scRNAseq_integration.ipynb" notebook, I have combined my MERFISH data with single-cell RNA-seq data and inferred t…
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Hi,
Is it possible to run gpsFISH without spatial count and spatial cluster datasets (or can it run with spatial count and cluster datasets provided in the tutorial)? I am working with the datasets…
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Hello!
I have some seqFISH data from Spatial Genomics generated by their 'genePS' system. I was wondering if anyone had some code to import this data into a SpatialExperiment S4 R/Bioconductor clas…
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Hello!
I have some seqFISH data from Spatial Genomics generated by their 'genePS' system. I was wondering if anyone had some code to import this data into a SpatialExperiment S4 R/Bioconductor clas…
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# Design
## Additions
For Assay
MUST Use
mCT-seq [EFO:0030060]
"cell" or "nucleus"
MERFISH [EFO:0008992]
"na"
…
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Hi~I'm a fresher and have a problem here. I can only successfully preprocess the example images from fq-segmentation. But when I use the example images from fq-imjoy or my images, it gives me wrong re…