Hi all thanks for the quick reply. Sorry about the delay, I was flying back home from visiting family for xmas…so ive been a bit distracted with jet lag!
I came across this and am looking at this as a posibility. I will have to convert my raw files to hdf5 (i think for terastitcher).
On Big stitcher, I used the file position names. If I downsized the file significantly and used virtual file option, the stitcher ran but failed to do any registration or stitching. I then tried to do slightly less downsizing, this would begin by opening (virtual) the first two files but would then get stuck on the 3 file every time. It would hold memory but not do anything. Maxing out my ram. (12GB available to fiji). When I ran with a massive amount of downsizing, the ram wasnt particularly taxed. You have made me think though, the downsizing should have worked. I have assumed (due to file naming) that I have 5 columns with the spacing as (x1, y1), (x2, y1), (x3, y1), (x4, y1), (x5, y1).
The failure in the down sizing, should have registered and stitched (a bad version) at least. Which may suggest that the columns may be wrong. I will have a go at trying it rows instead with the spacing as (x1, y1), (x1, y2), (x1, y3), (x1, y4), (x1, y5). This will give a rough answer to whether the orientation are correct.
My images are 3d volumes from XCT. The original file format is raw, so if I work in python, i tend to convert to hdf5 or into zarr format. For the stitching, I have been converting the raw file to tiff, using fiji. This could be an issue i wonder in the conversion process. The #bigstitcher plugn doesnt read raw files and the docs advise converting to tiff.
I wonder if this has been something that the #python library image processing community should look into? #itk appears to have the capability but the docs are missing the #python examples/use case. #elastix seems much more towards registration and not registration and stitching beyond the size of the original fixed image. #scikit-image has a paper where they show feature based registration then use emblend to stitch the two images together. I have seen some note book examples of #scikit-image with 2d panorama stitching but not for 3d volumes. Since this is also needs to spill on to disk for my use case. It would be interesting to hear some thoughts on that… for the future
Oh but also to work out how i can stitch this now and we can discuss future cases…