Alignment of overlapping images

Dear Knime imaging experts,

we are looking for a simple way to fuse or align to images that partially overlap (in the x dimension). The images stem from a microscope. In order to image the complete object of interest (a fish embryo) with a high resolution, we have to take at least to photos. We thought that these two photos that are partially overlapping could be combigned using the "Align image" node. But regardless the configuration we used we always failed. There is not a very detailed description of the node available. Hence, maybe it is not suitable for the operation we had in mind.

We also thought about using an imageJ macro should the KNIME nodes not be suitable. Or could our image quality be not sufficient or the overlapping region not big enough (the background is very variable - which we could probably improve)?

Any hints or ideas would be greatly appreciated. Attached is an example workflow with a pair of overlapping images.

Kind regards



Just a follow up to my earler post today. We managed to fuse the images with an imageJ macro (Stiching), but we failed to implement this in a knime workflow and we do not know how to implement macros in the knime workflow. I have attached an example of a Knime workflow with an imageJ macro, the imageJ macro itself, the macro code and an example of a fused image (the light shadow in the middle indicates the fusion zone).

But maybe it is easier to do the alignment in KNIME directly instead of a macro. The macro also requires that the two images to be fused need to be located in two different folders. With a knime workflow and images from two different columns that could be much easier.

Thanks in advance


Hi Stefan,

we will try some things and let you know as soon as possible what we found. We are also working on stiching support directly within KNIME. We hope to have this functionality some time this summer.




Hi Christian,

just to let you know that we established a workflow with the external tool node (calling imageJ and the Stitching plugin). It is not ideal but hopefully in the future there would be a KNIME node to conduct the stitching.

Kind regards


Dear Stefan,

I tried to run your attached example, but it gives an error:

WARN  Regex Split          0:7        Not configuration available.

WARN  Align image          2:7        Problem occured in rowRow0 : Wrong number of valid shift dimensions '2' or dimensions do not exist in Image! Skipping Image Image_1 02_018--L01.tif Missing cell has been inserted

WARN  Align image          2:7        1 errors occurred while executing!

Can you reproduce this or am I doing something wrong?


And could you please explain the difference between:

"Dimension selection" (D) and "Shift dimension selection" (S)

In (D) I can select multiple dimensions and in (S) only one dimension.