Please help: Collaborative Standards for 3D BRAIN Microscopy

Hi everyone,

I have been part of a workgroup on collaborative standards for 3D BRAIN microscopy. We have been working hard on finding standards for tissue clearing protocols and for microscopy metadata. Now has come the time to ask you for your feedback on the metadata part (tissue clearing will come later). Please fill out the survey below! Thanks for your help!

Hope everybody is well
Jan Huisken

The Brain Initiative 3D Microscopy Working Group (WG) recognizes your expertise in microscopy and requests your feedback on proposed archival metadata standards. The WG has put significant effort into the development of these metadata standards. The expectation is that these metadata standards will be required for 3D microscopy datasets that are submitted to the Brain Image Library (BIL).

The proposed archival metadata standards are intended to promote consistent representation of 3D brain microscopy data among BRAIN Initiative investigators and the larger neuroscience community. Widespread adoption of these metadata standards will promote reuse of datasets, facilitate evaluation of microscopy experiments, and enable development of computational tools.

The archival metadata standards are the first of several community standards in support of 3D brain microscopy that will be proposed by the WG. In the near future, standards to more fully describe 3D microscopy laboratory protocols will be presented to the community for feedback. Details for sharing BRAIN Initiative data and use of these standards can be found in the Notice of Data Sharing Policy for the BRAIN Initiative.

Co-Chairs Alex Ropelewski, Pittsburgh Supercomputing Center and Jan Huisken, Morgridge Institute for Research, thank you on behalf of the BRAIN 3D Microscopy Working Group.
We value your feedback on the proposed archival metadata standards. More specifically, are they sufficient and easy to adopt? Please respond by May 12, 2020.

To provide feedback, click here.


Hi Jan,

I’ve filled in the survey, but just wanted to say that this is a great initative. There’s a surprising amount of metdata needed to properly analyse whole-brain images, so if this is adopted, it will make life much easier.

I’ve involved in the development of various whole-brain image analysis and visualisation tools (e.g. cellfinder, amap, brainrender), and I’d be very interested in supporting these metadata standards, and encouraging their use in the community.

I’ve also been in contact with other developers of analysis software in this space, and there’s a lot of enthusiasm for adopting open standards (for e.g. atlases, detected cell positions, transforms etc.) to allow interoperability of different analysis software. Is this covered in the scope of the working group?


Hi Adam

thanks for your help. You raise a valid point about the interoperability of different analysis software. This is aspect is not within the scope of this group, but I hope that the metadata standard will allow for entries that keep track of the relevant post processing that has been done on the data. This is also important for the reproducibility of the entire experiment: sample prep, (instrument design), image acquisition and processing. Ideally this should allow for different pieces of software to work hand in hand on the same data. Ultimately, information about segmentation and analysis results can provide feedback for the microscope to steer the next image acquisition. We are still in the process of testing different metadata strategies on our Flamingo microscopes to allow for such feedback.



Great, I look forward to the results.


Hi @Jan,

Such a great initiative. Metadata is so crucial in microscopy, but unfortunately still so underrated / underreported.

Currently, I am a member of BINA’s Working Group for Quality Control and Data Management led by Caterina Strambio De Castillia. The aim of the working group is to extend the OME metadata model (arXiv article).

It might be worth to reach out / combine forces.

Best wishes,


PS: I have already posted my feedback to your model

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Hi Jan,

Even if we cannot help with archival metadata standards, maybe we can help with 3D brain microscopy since our lighfield microscopy has interesting applicabily in this field.

Let’s talk!
Best regards,