[ome-users] Handling tiled images

[Robert Schuler]

I am having trouble figuring out how to handle large tiled images with Bio-Formats 5, OMERO 5, and ImageJ 2 (using Bio-Formats 5). The input format is Zeiss CZI coming from a new Zeiss Axio Scan.Z1.

It seems in all cases to treat the tiles as any other series of images, and in my test image there are some 423 series. It could very well be that I don't know what I'm doing...

In OMERO5, when uploading the image, it expands it to 423 images. Also, when trying to open any of those images, it says the image is corrupt, so maybe some trouble handling the pixel data.

In ImageJ2, when importing using the loci tools plugin (release 5), it asks which of the 423 images I want to open. So I cannot really view the whole image this way.

With bfconvert, I've tried to convert to JPEG2000, and it does seem to convert one of the series of images to a standalone JPEG2000. Ideally, there would be a flag so that I could convert the whole image rather than individual tiles/series.

With bfconvert, converting to JPEG fails:

./bfconvert ~/cirm/ip-test-file.czi ~/ip-test-file.jpg
/Users/schuler/cirm/ip-test-file.czi
ZeissCZIReader initializing /xxx/xxx/cirm/ip-test-file.czi
Unknown IlluminationType value 'Fluorescence' will be stored as "Other"
Unknown IlluminationType value 'Fluorescence' will be stored as "Other"
Unknown IlluminationType value 'Fluorescence' will be stored as "Other"
Unknown Immersion value 'Unknown' will be stored as "Other"
Unknown Immersion value 'Unknown' will be stored as "Other"
Unknown Immersion value 'Unknown' will be stored as "Other"
[Zeiss CZI] -> /xxx/xxx/ip-test-file.jpg [JPEG]
Exception in thread "main" loci.formats.FormatException: Unsupported image type 'uint16'.
	at loci.formats.FormatWriter.checkParams(FormatWriter.java:422)
	at loci.formats.out.ImageIOWriter.saveBytes(ImageIOWriter.java:94)
	at loci.formats.FormatWriter.saveBytes(FormatWriter.java:136)
	at loci.formats.ImageWriter.saveBytes(ImageWriter.java:205)
	at loci.formats.tools.ImageConverter.convertPlane(ImageConverter.java:545)
	at loci.formats.tools.ImageConverter.testConvert(ImageConverter.java:481)
	at loci.formats.tools.ImageConverter.main(ImageConverter.java:667)

In the past, with non-tiled slides, I've been using the Bio-Formats API directly to read pixel data from one series, which worked for our tools because that was basically the whole image. With tiled images, does Bio-Formats have an API for reading in a tiled series of images AS IF it were just a single image? Or what's the recommended way to get the tiles out, and make sense of them?

Thanks in advance for any help.

Rob