Stitching issue - possible to ignore metadata?

Tags: #<Tag:0x00007fd5430c1898>


I’m attempting to stitch a stack of images using the stitching plug-in in FIJI but running into problems that I believe are due to how the stitching interprets channels in the file metadata. The coordinates of the images are in the filenames as outputted from our microscope. There are two images in the y-axis and one in the x-axis.

I have attempted to do this using the plugins–>stitching–>Grid/collection stitching–>filename defined position

The filenames are of the following format, for example:
14-36-18_17f-37-05_calbindin_CB38a_Calbindin633_25ms_3-2m_10um_20ol_80per_Ultra[00 x 00]_C00_xyz-Table Z0000.ome.tif

Where the [00 x 00] defines the y and x coordinates and ranges to [01 x 00]. In the stitching pop-up for filename defined position I replace this with [{yy} x {xx}]

However, the images do not get stitched and I just get my original images back. There are two channels defined in the metadata, and it looks like the stitching algorithm is separately attempting to stitch these two channels. However, these two ‘channels’ are actually the y-coordinates. Is there a way to get the stitching program to ignore the metadata and only use the information from the filename to define the stitching parameters?