skip to content

Sainsbury Laboratory

Research Profile

My work focuses on understanding how plant shoots acquire their form, particularly in 3D. I employ an interdisciplinary workflow, mixing experimental, computational, and theoretical methods to gain a holistic understanding of developmental processes, and how they drive aerial morphogenesis. More specifically, I have worked on developing segmentation techniques on the tissue scale (the task of identifying the precise boundary of every cell in an image), which allows for high-throughput quantification of early flower organs, and their geometrical features – information that can also be connected to the geometric properties of the individual cells that make up the corresponding organs.

Illustration of the tissue-level segmentation workflow showing different processing stages, consisting of the 1) raw data, 2) contour, 3) surface mesh, 4) mesh curvature, and 5) the final, segmented mesh. From the segmented data, sub-tissue geometrical properties can be quantified.


I am also interested in the process of auxin transport in the shoot, and how it connects to the initiation of new flower organs. My work is particularly focused on the numerical quantification of PIN-FORMED1 (PIN1) auxin efflux transporters on individual cell membranes, and integrating this information with mathematical models of protein-mediated auxin transport. The connection between auxin maxima formation, PIN1 polarisation, and organ formation is a fundamental question in plant development, which my work seeks to untangle.

Example workflow for modelling auxin patterning in the shoot apical meristem. The figure shows 1) the raw data, 2) the single-cell segmentation, and 3) the resulting auxin patterning after simulation of a simple auxin transport model.

A significant part of my research is, finally, focused on the role of mechanical regulation in maintaining and driving shoot morphology. In particular, I am interested in the crosstalk between between the cytoskeleton and cell wall, such as between microtubules and cellulose synthase complexes in regulating mechanical feedback and material anisotropy. Proteins of particular interest are CELLULOSE SYNTHASE INTERACTING1 (CSI1), as well as members of the XYLOGLUCAN XYLOSYLTRANSFERASE (XXT) family. For this project, I again combine high-throughput quantitative analyses on the cell and tissue level, and investigate spatiotemporal geometric patterning.

Quantified cell eccentricity in 1) wild type, 2) pom2 (centre), and 3) csi1 (right) plants, showing the variation in patterning between wild type and mechanically compromised mutants. The images were made by registering multiple plant shoot images together to visualise the trends in patterning.


On the personal side, I enjoy hiking, photography, and playing chess.



Åhl, H., Zhang, Y. and Jönsson, H., High-throughput 3D phenotyping of plant shoot apical meristems from tissue-resolution data. Frontiers in Plant Science, p.712.

Bhatia, N., Åhl, H., Jönsson, H. and Heisler, M.G., 2019. Quantitative analysis of auxin sensing in leaf primordia argues against proposed role in regulating leaf dorsoventrality. Elife, 8, p.e39298. 

Merlevede, A., Åhl, H. and Troein, C., 2019. Homology and linkage in crossover for linear genomes of variable length. Plos one, 14(1), p.e0209712.


Research Associate
Henrik Åhl profile photo

Contact Details

Sainsbury Laboratory
University of Cambridge
47 Bateman Street
Cambridge CB2 1LR