Please help: Collaborative Standards for 3D BRAIN Microscopy - Tissue Clearing Feedback

Hello everyone,

Back in April, Jan Huisken posted a request from the working group on collaborative standards for 3D BRAIN microscopy for feedback on metadata standards: Please help: Collaborative Standards for 3D BRAIN Microscopy Thanks to everyone who filled out the metadata survey – your responses were very helpful and insightful!

The working group is now asking for your feedback on tissue clearing. Please follow the link below to fill out the survey.

Best regards,
Wayne Huggins

The BRAIN Initiative 3D Microscopy Working Group (WG) recognizes your expertise and requests your feedback to help guide tissue clearing protocol recommendations for the BRAIN Initiative. Standard tissue clearing protocols will ensure consistent data collection, improve data interpretation and facilitate data sharing among BRAIN Initiative investigators and the larger neuroscience community.

Currently, there are many tissue clearing protocols to choose from, and each is optimized for different use cases and performs differently across the range of evaluation factors (e.g., transparency, resolution, cost, speed, resolution depth, size change, tissue stability, etc.). To help quantity these differences, the WG is requesting information not readily available in the scientific literature, including:

  • Protocol efficacy and ease of use,
  • Negative results (instances when a tissue clearing protocol did not work),
  • Modifications to protocols needed for specific use cases,
  • Pre-processing and post-processing steps not specific to published protocols, and
  • User experiences stratified by analysis needs, tissue types, and labeling strategies.

The results of this outreach will inform the development of a freely available, Web-based tissue clearing resource. The WG also requests feedback on the functionality of this site, which could include best practices and tools to recommend tissue clearing protocols based on experimental parameters.

Feedback on tissue clearing protocols is the second community outreach effort presented by BRAIN Initiative 3D Microscopy Working Group. The first outreach, in May 2020, focused on archival metadata standards to promote consistent representation of 3D brain microscopy data.

Co-Chairs Jan Huisken, Morgridge Institute for Research, and Alex Ropelewski, Pittsburgh Supercomputing Center, thank you on behalf of the BRAIN 3D Microscopy Working Group.

We value your feedback on the tissue clearing protocols. Please respond by Friday, December 18, 2020.

To provide feedback, click here.