How to load a .oif file without converting into a different

I have captured a large number of images as .oif files (from an Olympus confocal microscope). I tried to load them into CellProfiler but it didn’t recognize the files, it would only recognize the files when I converted a few to tif. I’m using the Speckle couting pipeline and it worked very well with the tif files.

Is there a way to load .oif files into CellProfiler, or have CellProfiler recognize the .oif files without having to convert them into a different format?

Would be great if you could help me with this!

PS. In LoadImages, .oif doesn’t show up as one of the options, I could only find tif, tiff, flex, zvi under the “File type to be loaded”.

Hi Susana,

CellProfiler uses Bio-Formats to read image files, and .oif is listed there so in theory CP can directly read it. However the current release version of CP (11710) may not show all filetypes. So, if you like, would you:
(1) Please upload an example .oif file here, so we can test it. I don’y have access to a file like this, so I cannot reproduce the issue. (zip up the file, in case the Forum complains)
(2) Try an updated version of CellProfiler “trunk build” here. (Please read the caveats!). I suggest the 2.0 version since the UI has not changed, and for now avoid the 2.1 version on the Trunk Build page.

We will be releasing a new version in the next couple of months (hopefully on the short side of that) which ought to work for you, but you can at least do some testing with an updated version.