search

FrancisCrickInstitute / Phenix_HCS_Imagestitcher

This is a data-science pipeline that allows for stitching/mosaic'ing of images collected from a PerkinElmer HCS such as Phenix so that you can start interrogating your macroscale data
Other
0 stars 0 forks source link

stitching PE Harmony 5D dataset #1

Open atarkowska opened 5 years ago

atarkowska commented 5 years ago

Hello, I am trying to run PE_phenix_stack_stitcher.py on 40x 4 channels 25 Z-stack, but I am facing issues with stitching. First becuase of hardcoded coordinates in https://github.com/FrancisCrickInstitute/Phenix_HCS_Imagestitcher/blob/master/src/tools/image_stitcher.py and second becuase it looks like Z-stack is not supported. Is this something you would consider upgrading?

ajay-bhargava commented 5 years ago

Thanks for your question, yes it is something i'm looking to upgrade. Z stack is currently not supported since the dictionary extractor isn't capturing the data, though it could. When developing this algorithm, I didn't have a z stack to work with so i couldn't test it out. A dataset would be helpful!

As for hardcoded coordinates, one approach would be to do SIFT and RANSAC matching. Another would be to know the degree of overlap and apply it to the coordinate register for each image to be stitched.

Happy to receive pull requests if you want to implement this. My mission for this script was to liberate the data acquired from the PE Phenix, and i hope we can build something to get to this goal.