Image dimensions compatibility IJ and Knime

Dear all,

reading in imageJ data saved in Knime causes some headache. Example image is a XYZ stack, 1 time point, 1 channel.

First of all one should take care of the pixel type. It took me a moment to understand that UNSIGNEDSHORTTYPE <-> 16 bit and UNSIGNEDBYTETYPE <-> 8 bit. Plain BYTETYPE gives a 32 bit image in imageJ.

The dimensions are only correctly read if I use the SCIFIO option (IJ2) in imageJ. If I use Bioformats or plain IJ1 the Z and T are swapped and I loose the calibration data.

I tried to save in OME.tif, which in my expectation should be compatible with bioformat importer, but this was of no help. I also swapped Z and T in Image-Writer and change the bioformat import options (XYZTC or XYZCT).

I use IJ version: 2.0.0-rc-69/1.52p and Knime 4.1.2

save_labeled_image.knar.knwf (17.1 KB)
blobs-3d.tif (2.6 MB)

1 Like

Hi @apoliti,

I am very sorry for the late answer, but I hope I can give you a satisfying explanation for the origin of this issue. KNIME Image processing uses SCIFIO for writing images, this is why reading using the SCIFIO importer usually works the best. This is especially the case for tif images as the SCIFIO has a slightly different implementation of it than the plain ImageJ reader.

Why do you especially want to use the bioformats importer in imageJ?
best,
Gabriel