ImageFeaturePlot can not show when data is huge

[Chaosli98]

Hi,
First of all, thank you for developing such a great tool! I am new to seurat V5, and i just start to use this for MERSCOPE data. So far I've been able to reproduce the tutorial data pretty well, which is only 80,000 cells.

However, I recently got more than 800, 000 cells in a slice, and I couldn't get any gene expression in any one cell when I used ImageFeaturePlot, just got axes and a black backgroud. I sure that the genes were fine, and the other drawing features including ImageDimPlot and FeaturePlot worked fine. Is it because there are too many cells? Any suggestions for how to deal with it?

Thanks!

Jin

[alikhuseynov]

Hi,
Could you provide an example of your script for ImageFeaturePlot?
What type of segmentation data from Vizgen do you have, eg in .parquet file?
Take a look these:

• Processing vizgen data #7080
• Support to handle .parquet output from Vizgen #7190

it was tested on a number of Vizgen data. (Note: that is NOT Seurat V5)
See if you can load your data and do plots.
hope this helps

[Chaosli98]

My segmentation data are json files, and I can be sure that there is no problem with my data reading. For the tutorial data, ImageFeaturePlot works well,

I can do other plot such as "FeaturePlot(vizgen.obj,features = c('CD1C'))", and "ImageDimPlot(vizgen.obj, fov = "BC", cols = "Set3", axes = TRUE,size = 0.3,alpha = 0.5)". However, for ImageFeaturePlot, i do it by "ImageFeaturePlot(vizgen.obj, fov = "BC", features = "PECAM1")", only got axes and a black backgroud.

[alikhuseynov]

Try non capital letters for gene names, like you did with `Set3`, ie, would be `Pecam1`. As for the coord scale, if you load Vizgen data, then those will be in microns units for the axes

[AustinHartman]

@Chaosli98 While ImageFeaturePlot is a bit slower for plots with extremely high numbers of cells, I'm still able to generate plots with expression for a dataset containing 885K cells. Are you attempting to plot expression for each cell segmentation or each cell centroid?

[dcollins15]

Thanks for using Seurat!

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