mesoSPIM in 2021: year wrap up

1 minute read

Dear mesoSPIM users, 2021 was hard for many of us, and I hope you come to the year end in a good shape. Before the holidays start, I would like to recap the mesoSPIM developments this year, and give an outlook for 2022.

Change of the core developer

Fabian Voigt has moved to a new position at Harvard (Engert Lab) to work on live zebrafish brain imaging. We all miss his expertise and energy that made the mesoSPIM project possible! I stepped in as the project developer in June, and am very excited about growing it further. My challenges are both local and global. Locally, I maintain and develop mesoSPIMs as a platform for AdaBD Program, and for Zurich bioimaging community. Globally, I work on the code, documentation, and tutorials to broaden the mesoSPIM adoption. It is a job with many hats, so I apologize if some developments were slow.

Software updates

I made two major releases, in July and November. Many bugs were fixed, and new features were added, with the user convenience in mind. For example, autofocus, saving in TIFF files, simplified installation and launching were implemented. Full list of changes can be found in the project github. Unlike Windows, updating mesoSPIM really brings new features and fixes old bugs, so try it out.

Managing large multi-tile/channel datasets

Many improvements were made in the Tiling Wizard to streamline the acquisition process. To help you manage complex datasets, I created a YouTube video tutorial, which guides you step-by-step from raw data (H5 file with multiple tiles and channels) to saving TIFF files of stitched and fused images, with (almost) no stitching marks, via Fiji/BigStitcher software. So, if you want to image with high magnification, samples that do not fit the field of view, this tutorial is for you.

March User Meeting

On March 10, we are planning a one-day user meeting, with topics covering modern clearing techniques, mesoSPIM user workflows, and image processing methods. The format will be hybrid, online plus limited personal attendance (if allowed in the pandemic situation). The program will follow soon, so save the date!


Nikita Vladimirov