MERFISH sample id on BIL

Technical
1

Hi, I was looking for MERFISH mouse brain raw data on BIL, however was struggling to assign the correct samples. Any documentation/clarification would be appreciated!

  1. ABC Atlas (Yao 2023 Nature) links to https://doi.brainimagelibrary.org/doi/10.35077/g.610, which contains three folders (609882, 609889, 638850). Each contains serial coronal sections. I was assuming 638850 is the one used by Yao et al., which ones are the others then? Or are these all from the same animal?

  2. Zhang 2023 Nature (data also used in ABC Atlas atlas above) links to https://doi.brainimagelibrary.org/doi/10.35077/act-bag. This folder contains coronal and sagittal sections from 4 animals. I found that the /data folders containing raw .dax images are much smaller than expected (few GB compared to expected few TB). Is this possibly incomplete data?

Thanks!

2

Hi Simon,

To your first question. You are correct, 638850 is the dataset used for the abc atlas. The other two datasets are ones we collected earlier from different mice. They have a different gene panel optimized for an earlier, forebrain specific taxonomy. They also collect section at a smaller interval that only covers the central parts of the brain.

For your second question, I can only speculate you would have to reach out to the Zhuang lab, but I think those dax files are the individual imaging tiles for all rounds, so you would have to run the decoding yourself.

Michael

3

Hi Michael,

Thanks for the quick reply, that is very useful.

Best, Simon