gitdemont
commented
1 year ago Hello @wooksh ,
Thanks for your interest and kind words about IFC package.
Currently only 30817 and 30818 compression format are supported.
My guess is that your .daf file and the associated .cif file from which you are trying to visualize images were generated with IDEAS® >= 6.3 where 30819 may be used. One solution should be to generate those files with previous version of IDEAS® software.
However - not 100% sure - you may be able to visualize the images from .rif file though.
Besides, with the line rif <- readIFC(daf_file_path), you have read and stored a lot of usefull information from your .daf file into the rif variable (NOTE that this is confusing, I would have named it daf)
| Element | Description | Further use |
|---|---|---|
| rif$description | details about the software version, image display settings, masks, file | str(rif$description) |
| rif$features | data.frame of the features values for each cell | prcomp, write.csv, FlowSOM::SOM # whatever you need |
| rif$regions | names, vertices, colors, ... of regions/gates drawn | popsNetwork(rif) # to explore population hierarchy and gating iformation |
| rif$pops | information about populations created and objects/cells membership | popsNetwork(rif) # to explore population hierarchy and gating information |
| rif$graphs | graphs details (not easy to read/understand) you can use to plot in R | plotGraph(rif, rif$graphs[[ii]], draw = TRUE) # where ii is your graph number |
HTH
Hello,
At first, I'd like to thank the authors for creating this very useful and needed tool. While trying to visualize cells from ImageStream, I've encountered the following error: "hpp_decomp: can't deal with compression format: 30819"
This is the full script I am using: `library(IFC)
setwd("/home//Desktop/FlowCytometry")
daf_file_path <- "./IS_20221010_0041_MiZab/MalFl_221007_S1_3.daf"
rif <- readIFC(daf_file_path)
DisplayGallery(fileName=rif$fileName)`
I wonder, is it a matter of some codecs I need to install? Unfortunately, googling the error didn't bring any solution. I will appreciate any help.
Best regards