March 2025 Newsletter

March 03, 2025

By Jian Wei Tay

Contents

Image analysis update

As the Biological Image Analysis Group Leader, I am excited to share updates about some of our ongoing image analysis projects. I’m sure it comes as no surprise that we have been gearing up on AI - for both commercial and home-built approaches.

Screenshot from Imaris
Screenshot from Imaris showing how AI segmentation works. The broad green and magenta lines are user annotations, while the shaded areas are machine-predicted labels for foreground (cells) and background.

On the commercial side, we’ve been testing and creating new pipelines for the AI segmenter in Imaris. Our testing is showing that the tool could be useful to refine surfaces for complex shapes or when working with objects of different intensities. We’ll be putting up documentation on how to use this tool soon on our Wiki.

We also recently published a new tool named Cypose, developed by Clair Huffine and Zachary Maas (IQ Biology), to improve segmentation of cyanobacteria. The new tool uses the Cellpose framework to generate fine-tuned models to identify brightfield images of cyanobacteria. The paper was published in Photosynthesis Research.

We are now using some of the methods mentioned here on other projects, and we’ll share more as the year progresses. I am also presenting a workshop on Imaris at the annual meeting of the ABRF in May.

If you are interested in learning more about AI and how it could potentially help with your research, please reach out.

Project VIABLE

Over the past two years, the ALMC has also been embarking on a number of educational initiatives. Our imaging wiki is an example of this. Another example is Project VIABLE, which is building interactive computer simulations of the microscopes in the facility to help with training. Development on this project is funded by a CU ASSETT grant and is primarily carried out by Computer Science capstone students.

We’re hoping to have a fully usable demo by the end of the academic year, but here’s a screenshot teaser in the meantime.

Screenshot showing simulated microscope controls
Screenshot from our work-in-progress microscope simulation module. The team has got zoom, focus, and joystick control and is working on adding in intensity settings to the simulation. We're also working on new graphics to spruce things up.

Recent publications

If you have published recently, please let us know.

  1. Clair A. Huffine, Zachary L. Maas, Anton Avramov, Christian M. Brininger, Jeffrey C. Cameron, and Jian Wei Tay. Machine learning models for segmentation and classification of cyanobacterial cells. Photosynthesis Research 163, 16 (2025). Image analysis.

  2. Wyatt C Powell, Ruiheng Jing, Morgane Herlory, Patrick Holland, Darya Poliyenko, Christopher C Ebmeier, Michael HB Stowell, and Maciej A Walczak. Chemical Synthesis Reveals Pathogenic Role of N-Glycosylation in Microtubule-Associated Protein Tau. Journal of the American Chemical Society 147, 6995-7007 (2025). A1R laser scanning confocal.

  3. Alexandra N Borelli, Courtney L Schultze, Mark W Young, Bruce E Kirkpatrick, and Kristi S Anseth. Ligand presentation controls collective MSC response to matrix stress relaxation in hybrid PEG-HA hydrogels. Bioactive Materials 44, 152-163 (2025). Spining disk confocal.