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labsyspharm / ashlar

ASHLAR: Alignment by Simultaneous Harmonization of Layer/Adjacency Registration
https://labsyspharm.github.io/ashlar/
MIT License
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Inconsistent tissue for same tile across cycles #217

Open josenimo opened 1 month ago

josenimo commented 1 month ago

Dear ashlar devs,

I have been optimizing ashlar for a TMA CycIF dataset, 5 cycles, 30 channels. Now I have very good parameters that I am planning to scale to the rest of the dataset, but I have a small issue that I kind wrap my head around.. and was wondering if there is a simple solution to. Corner tiles of my TMA cores are consistently being misregistered. I think it is because of inconsistent presence of tissue in these tiles, from what I can only assume are slide holder shifts between cycles. See picture below:

Screenshot 2024-05-17 at 10 23 33

See full QC report here: 20240515_HN46_Core05_QC.pdf

Thank you for your feedback! Happy to provide more context and qc if you think it would help

josenimo commented 1 month ago

Just to let you see all the cycles, and the stitching quality: Screenshot 2024-05-17 at 10 36 15

Yu-AnChen commented 3 weeks ago

Hi @josenimo, not sure if this post is under your radar - https://forum.image.sc/t/how-to-estimate-ashlar-barrel-correction-parameter/79719

We've noticed that the lens distortion is most sever on the edge of each tiles. Jeremy's script uses a simple model to correct it and after correction, the stitching and registration result are usually improved. I suspect you might need this because the absolute tile position in cycle 2 is quite different from cycle 0.