### I: Human Lung: Nanostring CosMx Spatial data analysis in Seurat library(Seurat) library(tidyverse) ### 1. loading the data # lung5-rep1-demostration data # nanostring.com/products/cosmx-spatial-molecular-imager/nsclc-ffpe-dataset// # the coordinates for the cell boundaries # www.dropbox.com/s/hl3peavrx92bluy/Lung5_Rep1-polygons.csv?dl=0 nano.obj
Thanks you so much, it is very helpful. I analyze my data with your code, but always give me an error with this code “ ImageDimPlot(nano.objb, fov = "b", cols = "glasbey")”. It said “ No compatible spatial coordinates present”. Which files save this information? I have all the files as yours ( including the polygons csv file). But I noticed my CellComposite .tif file size is 284kb, yours is 7.3M. Is that means we lost spatial coordinates information? Is this the reason that I run R code failed? I hope you can see my message, and kindly reply me.
Would it be possible to do the CosMX seurat for Pancreas - stuck at the first ImageDimplot with the error - Error in ImageDimPlot(nano.obj, fov = "Pancreas", cols = "glasbey") : No compatible spatial coordinates present and also > ImageDimPlot(nano.obj, fov = "Pancreas ", nano.obj, fov = "Pancreas-CosMx-WTx-FlatFiles", cols = "glasbey") Error in ImageDimPlot(nano.obj, fov = "Pancreas ", nano.obj, fov = "Pancreas-CosMx-WTx-FlatFiles", : formal argument "fov" matched by multiple actual arguments
@@Collection_of_online_tutorials Hahah - if you could help with the code that would be amazing- think from following this tutorial I could do it or a video could also be amazing!!
@@Collection_of_online_tutorials Oh, I saw your comment late.. I heard that COSMEX data is not a transcriptome data. It's similar to protein data right? I saw the COSMEX can convert to Seurat Obeject and available dimension reduction too. Is it possible function analysis such as like DEG or GSEA? And can you reviewd CODEX data?
Hello, Sorry to bother you but the dropbox where the cell boundaries were seems to have been deleted, would you know how I can access the cell boundaries for the whole lung cancer dataset? Thank you for your help!
the cell boundaries were provided by Nanostring by request, you can email Nanostring, alternatively, you can use the Giotto pacakge which doesn't need the cell boundary files.
### I: Human Lung: Nanostring CosMx Spatial data analysis in Seurat
library(Seurat)
library(tidyverse)
### 1. loading the data
# lung5-rep1-demostration data
# nanostring.com/products/cosmx-spatial-molecular-imager/nsclc-ffpe-dataset//
# the coordinates for the cell boundaries
# www.dropbox.com/s/hl3peavrx92bluy/Lung5_Rep1-polygons.csv?dl=0
nano.obj
Wow wow ow!! Awesome tutorial indeed. God bless you professor 🎉😊
Thanks for making this and sharing the commands here. This extremely helpful...
Thank you!!!
Wow❤
💯
HI, thank you. Dont you have to do QC for the data?
hi, thankyou for the wonderful tutorial! im just wondering, do you need to use those csv files in the raw Nanostring output?
Thanks you so much, it is very helpful. I analyze my data with your code, but always give me an error with this code “ ImageDimPlot(nano.objb, fov = "b", cols = "glasbey")”. It said “ No compatible spatial coordinates present”. Which files save this information? I have all the files as yours ( including the polygons csv file). But I noticed my CellComposite .tif file size is 284kb, yours is 7.3M. Is that means we lost spatial coordinates information? Is this the reason that I run R code failed?
I hope you can see my message, and kindly reply me.
Could you do stereo-seq analysis?
Would it be possible to do the CosMX seurat for Pancreas - stuck at the first ImageDimplot with the error - Error in ImageDimPlot(nano.obj, fov = "Pancreas", cols = "glasbey") :
No compatible spatial coordinates present and also
> ImageDimPlot(nano.obj, fov = "Pancreas ", nano.obj, fov = "Pancreas-CosMx-WTx-FlatFiles", cols = "glasbey")
Error in ImageDimPlot(nano.obj, fov = "Pancreas ", nano.obj, fov = "Pancreas-CosMx-WTx-FlatFiles", :
formal argument "fov" matched by multiple actual arguments
I have one, but not recorded🤭
@@Collection_of_online_tutorials Hahah - if you could help with the code that would be amazing- think from following this tutorial I could do it or a video could also be amazing!!
OMG, It's very helpful !! Can you available teach about CODEX spatial data too ?
could do
@@Collection_of_online_tutorials Oh, I saw your comment late.. I heard that COSMEX data is not a transcriptome data. It's similar to protein data right? I saw the COSMEX can convert to Seurat Obeject and available dimension reduction too. Is it possible function analysis such as like DEG or GSEA? And can you reviewd CODEX data?
CosMx has protein data too, at the moment, it anlyze 64 proteins, yes I will make a video for Akoya PhenoCycler (CODEX) data
Most gene and protein pannels are cell type specifc markers, it is difficult to do GSEA anlysis.😆
Hello,
Sorry to bother you but the dropbox where the cell boundaries were seems to have been deleted, would you know how I can access the cell boundaries for the whole lung cancer dataset?
Thank you for your help!
the cell boundaries were provided by Nanostring by request, you can email Nanostring, alternatively, you can use the Giotto pacakge which doesn't need the cell boundary files.
@@Collection_of_online_tutorials thank you! Do you have an email adress or should i use their site to contact them?
a