I have a single tiff file containing multiple time points, ‘fields’, montage tiles, z-slices and channels. It was made by Andor iQ software.
By ‘fields’ I mean multiple positions on the microscope stage (e.g. representing multiple samples) and a montage array of the same shape has been imaged at each of those fields.
I’ve been trying to simply stitch each field separately using a combination of the Bio-Formats importer and Grid/Collection stitching plugins but haven’t found a solution. The best I have managed so far is when in the stitching plugin I choose:
Type=Positions from file
Order=Defined by image metadata
In this case the multiple fields are all stitched correctly into the same image but with huge black spaces between them (I guess this is representing the real distance between samples). What I would want as output is separate images for each stitched field.
One problem is that with Bio-Formats all the tiles and fields are read as separate ‘series’… I can’t find a way to separate fields in Bio-Formats like you can with channels/focal planes/timepoints.
One solution would of course be to make a macro which separates out the fields before applying the stitching but there are some complications with this too like losing the metadata and (?) needing to save the individual field files before stitching.
So I’m mainly wondering if I’m missing something, like a way with Bio-Formats to automatically separate the ‘tiles’ from ‘fields’?
Many thanks in advance for the help,