Issues opening three-dimensional oir files with Bioformats

Hi all,

I’m trying to open multichannel, z-stack, time-lapse images in Fiji using the bioformats importer, and they are not opening properly. Some of the images are very large, and Olympus has split them into chunks (tdeos+3+3_A01_G010_0001.oir, tdeos+3+3_A01_G010_0001_00001, and so on).

For the smaller images, where everything is contained in one .oir file, Fiji only opens the first timepoint (with the z and channel information retained). Importing with different viewing options doesn’t seem to help (even the 1D default ImageJ viewer doesn’t contain any frames after the first timepoint).

When opening the larger, split files, the time-lapse component opens fine, but only for the last part of the movie. The first timelapse image is present, but the next ~35 are missing: Fiji throws a [WARN] No pixel blocks for plane #6094 error and the images themselves are blank. I think these missing images are in the first file “chunk” (the one ending with oir). But the channel, z-stack, and time dimensions are all present, unlike the smaller files. If I move the first .oir file to another location, ie my desktop, the time-lapse information doesn’t open, like other small .oir files. So bioformats must be reading the time-dimension correctly for large, split files, but not small, unsplit ones??

I’ve successfully opened both multichannel, z-stack .oir files and time-lapse, z-stack, files (both split into multiple files), so assume the third dimension is causing problems.

For both filetypes, trying to convert the files into .tiff using bfconvert also throws the following error:
[Fatal Error] :1:35: Character reference "&#0" is an invalid XML character. Exception in thread "main" java.lang.RuntimeException: org.xml.sax.SAXParseException; lineNumber: 1; columnNumber: 35; Character reference "&#0" is an invalid XML character.

The issue resembles the one reported here. (My bioformats version is 6.2 so should have this fix).

Has anyone had similar problems? Any suggestion for a fix or workaround? Probably the best thing to do at this point is export them as a .tiff from the microscope itself, but that may take several hours… Another thing to try is the OlympusJ plugin, but I’d have to borrow a colleague’s computer as the plugin isn’t compatible with Linux.

Any suggestions or advice would be greatly appreciated!

Hi @Shannon-E-Taylor, would you be able to upload sample files showing these issues along with a description of the expected dimensions to https://www.openmicroscopy.org/qa2/qa/upload/ for the Bio-Formats team to test

Hi @dgault,
Absolutely!
I’m uploading two examples of the smaller files I’m talking about. However my larger files are greater than the 2GB limit- is there a way around this?
Thanks so much for all you and the bioformats team do :slight_smile:

Thanks Shannon, we received the 2 first files, if you send me a PM on here with an email address then I can arrange for ftp access to transfer larger files.