A major requirement for our success has always been the integration into a strong multidisciplinary environment. Embedded in a scientific community that supports and challenges us, we have been most successful. For innovations in imaging instrumentation, we rely on strong ties to the physics, optics, microscopy, hardware, and software development communities. For our biological projects, we take inspiration from areas ranging from fundamental biology to medical applications. Both in vivo techniques and fixed and cleared tissue imaging have found many applications inside and outside our lab and have been trans-formative in a wide range of applications. Last but not least, data analysis and visualization are more important than ever, and therefore we seek input and support from the computer science community as much as we can. Smart microscopy and machine learning are becoming essential parts of our workflow to tackle the most interesting questions in fundamental cell and developmental biology as well as in clinically relevant biomedical imaging.

Microscope development

The overall goal of the Huisken Lab is the systematic study of developmental processes in living organisms by custom non-invasive biomedical imaging techniques. Over the years we have developed and perfected imaging tools that offer unique possibilities for the analysis of vertebrate development. The major aim of these efforts has been to push the limits of spatial and temporal resolution while maintaining the living specimens under physiological conditions.

Cell organization in early embryos

Morphogenesis is a dynamic process on many scales, governed by the shape changes, movements, divisions, and interactions of cells. For an understanding of the underlying biological mechanisms, it is therefore desirable to simultaneously capture the dynamic behavior of cells and their interactions across the entire embryo over long periods of time. Imaging a single embryo with high spatial and temporal resolution will reveal details of the developmental processes in the specific embryo under observation; however, the plasticity and variability of these developmental processes can only be addressed by imaging and analyzing a large number of samples.

Flamingo – democratizing access to high-end microscopy

We are developing Flamingo, a shareable, microscopy platform driven by direct involvement of the biological community under our guidance as developers. Since biological samples ideally should not travel, each microscope can be configured for an application, sent to the biology lab, and subsequently returned and reconfigured for another. Employing modularity in the design facilitates reconfiguration and allows easy upgradability and an expanding functional palette. We intend this open science platform as a framework for future collaborations and to

Cardiac morphogenesis and function

We have developed several tools to visualize and manipulate cardiac morphogenesis and function. For a systems-level understanding of cardiac structure and function, in particular, during early development, we need to characterize the function of every single cell, in its specific position within the myocardial network, to understand the emergence of whole organ activity, ideally mapped non-invasively and under physiological conditions in an intact animal.

Smart microscopy

When acquiring data from a large collection of biological samples, these data need to be integrated into a unifying model to learn about the fundamental, underlying and conserved developmental programs and to understand how each embryo differs from the rest. Acquiring these data blindly and waiting with the analysis until after acquisition is completed, bears the risk that large amounts of redundant data are acquired. It is therefore advisable to train the microscope to look out for differences when recording data from many samples for later comparisons.