I’m trying to run this program called BaSiC (an imagej plugin) that attempts to correct the discontinuity in between tiles and generates a more seamless image. However, I’ve run into a problem with the stitching portion using the Grid/collection stitching plugin on the corrected image sequences. Let me try to walk you down the pathway of this entire algorithm.
First, I’m taking the raw .czi files directly from Zen and importing them through BioFormats as a concatenated and single channel image sequence. Then, I’m saving this as an image sequence and running the BaSiC plugin. It generates an image stack of the corrected tiles which is then saved as another image sequence.
Now, the whole problem comes when I want to stitch these tiles together. In the Grid/collection stitching plugin, there are several options on the arrangement of the tiles and how to stitch them (ie grid: row by row, etc). Since my images aren’t perfect squares or rectangles, I need to select the option “positions from a files.” In doing so, I’m hoping that it can take the positions from the metadata and stitch the tiles properly. However, the format for the metadata from Zen is not the same format for the positions to be used in the stitching. Could you help me translate the metadata into a usable format for the Grid/collection stitching plugin?
Stay safe and thanks for your help!