There are two issues you’re dealing with right now; file size and file format.
To deal with file size, I would recommend either tiling your image into subimages or selecting a subset of fields to analyze. Remember that if you’re using very large images, you’ll need either a lot of time or a lot of computing power to analyze them.
As for the .svs file format issue, there are a few possible options:
- Use Aperio ImageScope (aperio.com: free download) to Extract Region (the button next to the pen tool). This gives you the option of extracting to a single large TIFF, extracting to tiled jpeg images (CWS), or others. Remember that TIFF images have a maximum image size of 4GB (compression won’t help) and that 32 bit operating systems can’t open images larger than 2GB.
- Contact Aperio and obtain a copy of either Digital Slide Studio or the Icomp.exe command line tool. These tools should be installed on systems with Aperio Spectrum.
- Utilize the other methods described below.
[quote=“ahbeck”]Dear CP2.0 Help,
Does CellProfiler support .svs images (such as those produced from whole slide scanners from Aperio: loci.wisc.edu/bio-formats-fo … o-svs-tiff)?
Here is an example file (they tend to be huge – 500 -1000 mb):
tcga-data.nci.nih.gov/tcgafiles/ … 00-DX7.svs
It seems there might be support for svs images in cellProfiler through BioFormats? (svn.broadinstitute.org/CellProf … init_.py).
Is it possible to directly read svs images into a cp pipeline?