Coordinate systems for microscopy

There is a BIDS extension proposal to accommodate microscopy images. This will help the community share data in a standardized way. More details here: .

In order to make this new standard as widely applicable as possible, we would like to get a better understanding of use cases in the wider histology community.

In particular, we are keen to understand how different users encode the spatial location of multiple files coming from the same sample. For example, when stitching images together within the XY plane, or creating a Z-stack stack of images in 3D.

The key question is: when collecting several images from the same sample, do you rely on an intrinsic coordinate system from the microscope? If so, how is this coordinate system encoded: is it in the native proprietary file format? In a standard format like OME-TIFF? Or, do you rely on an external metadata file?

If there is no coordinate system, how then do you reassemble images?

Thank you in advance for your input and for helping us create a data standard for our community.

Feel free to share this post with any relevant groups. Here is a cross-linked post asking the same question to the community: Call for comments on Brain Imaging Data Structure - Data Management - Forum