using Basic corrected tiles as input for ashlar

[janinemelsen]

Hi! I am applying cyclic immunofluorescence and would like to try ashlar to stitch and align the images.
I have been using Basic in ImageJ (flatfield correction only) to correct for shading correction of each individual tile, as derived from a czi file. For each individual cycle I have a folder with the individual tiles named (C1_001, C1_002 etc) for which C represents the channel, and the 001 the position of the tile. This grid consists of 9x10 tiles with 20% overlap.

I have been trying to use ashlar on one cycle by applying the following code:

ashlar "fileseries|/exports/klim-hpc/Janine/ENT067_cycle1|pattern=C{channel:1}_{series:3}.tif|overlap=0.2|width=9|height=10|pixel_size=0.445|layout=snake"

However, I ran into the following error: "images must be same shape" (after phase cross correlation)
Is there any way by which I can solve this?
And as a next step, how do I make sure that Ashlar recognizes the individual cycles and aligns them?

Thanks!

Janine

[emmanuel-contreras]

Hello, I am also running into this same issue on version 1.17 of ashlar. In my case I have CODEX images in a 5x5 grid that I'm trying to assemble. Ashlar seems to find the images but also fails in the phase_cross_correlation function ( see trace stack below) I print out the shape of the images that are being fed into the function but I'm not sure how to resolve the issue. Images are normally 1344x1008. I tried using images before and after running BaSiC but still got the same error which I would expect given that the image shape is the same. Let me know if you need more info, thanks!

[emmanuel-contreras]

I was able to get this up and running on the latest docker image, I tried the same images on 1.17 and got the same error as above, this seems to be an issue with this version 1.17. Also exporting as ome.tiff will result in imagecodecs error as in #174 but exporting as tiff works fine.

docker run -v './ashlar_inputs':/input -v "./ashlar_outputs":/output -it labsyspharm/ashlar:1.18.0b3 ashlar "filepattern|/input/reg005/t001|pattern=reg005_X{col:02}_Y{row:02}_t001_z001_c{channel}.tif|overlap=0.3|pixel_size=0.377454" -o /output/reg005.tiff --output-channels 0