I’ve noticed an issue when reading and writing tifs in KNIME using the either the table reader or image writer nodes. While everything works perfectly within KNIME the issue comes when reading a Fiji saved tif in KNIME or writing a tif in KNIME and then reading it in Fiji.
Here is a link to small workflow that highlights these issues.
In the top row, I read in two images (xyz) and merge them into xyzt. Then I write this to tif. If I open this image in Fiji then I get an xyt image with the z and t dimensions merged. However, if I open this in KNIME, I get the correct xyzt image.
The reverse case also occurs. If I start with an xyzt tif image saved from Fiji 4D.tif (158.8 KB) and read this in KNIME then I only get an xyt image. So I suspect that there is a disconnect between SCIFIO in KNIME and Fiji somewhere.
Of course it is relatively trivial to solve this in KNIME or Fiji by rearranging the dimensions. However, it would be great if the images could be read correctly in the first place. If anyone has an idea of what is happening here, that would be awesome.
Some basic troubleshooting:
This is not resolved by using the “Bioformats importer” in Fiji.
Moving the dimensions around or adding new dimensions in KNIME doesn’t help either.
This does not occur with the ICS image format.