SegmentedCell function

[HaefligerSimon]

Hi, I have a small issue with the SegmentedCell function in the spicyR package. It seems that in the new version of the package (version 1.17.10), this function is no longer present. Can you confirm this and possibly suggest a solution?

[alexrunqin]

Hi! Thanks for the feedback with our package.

As of 1.17.0, the SegmentedCell function and SegmentedCells as an object has been deprecated and is no longer in use. spicyR now operates primarily using SingleCellExperiment and SpatialExperiment objects.

Could I ask what you were using the SegmentedCell function for? There's likely now a new function which replaces its functionality.

Best,
Alex

[HaefligerSimon]

Hi, thanks for the quick response. I wanted to follow these line of code here : "### Something that resembles cellProfiler data
set.seed(51773)
n = 10
cells <- data.frame(row.names = seq_len(n))
cells$ObjectNumber <- seq_len(n)
cells$ImageNumber <- rep(1:2,c(n/2,n/2))
cells$AreaShape_Center_X <- runif(n)
cells$AreaShape_Center_Y <- runif(n)
cells$AreaShape_round <- rexp(n)
cells$AreaShape_diameter <- rexp(n, 2)
cells$Intensity_Mean_CD8 <- rexp(n, 10)
cells$Intensity_Mean_CD4 <- rexp(n, 10)
cellExp <- SegmentedCells(cells, cellProfiler = TRUE)" I have IMC data and I am working with a SingleCellExperiment object and I want to compare the cell-to-cell interaction between two group of patient. Is there a another way to run this? Thanks in advance for the feedback

Best regards

Simon

[ellispatrick]

Hi SImon,

If you've got your data into a SingleCellExperiment then you've done all of the hard work. Now you just need to tell spicy which columns in your colData() have information about your grouping structure (condition), your images (imageIDCol), cell type labels (cellTypeCol) and the x-y coordinates (spatialCoordCols).

If you have one image per person:
result <- spicy( cells, condition = "mygroups", imageIDCol = "imageID", cellTypeCol = "cellType", spatialCoordCols = c("x", "y"))

or if you have multiple images per person:
result <- spicy( cells, condition = "mygroups", subject = "subjectID", imageIDCol = "imageID", cellTypeCol = "cellType", spatialCoordCols = c("x", "y"))

[HaefligerSimon]

Great, thanks a lot for your help! Best regards, Simon