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Smart Multimodal Microscopy for High-Throughput Developmental Biology in Real-Time

Periodic Reporting for period 2 - SmartMic (Smart Multimodal Microscopy for High-Throughput Developmental Biology in Real-Time)

Reporting period: 2017-01-01 to 2018-06-30

Fluorescence microscopy is a key technology in our quest to understand fundamental developmental processes of life. High-resolution images recorded in intact, living organisms deliver insights into the complex interplay of molecules, cells and tissues in real time. Even though the resolution of microscopes has been pushed beyond the diffraction limit, providing important insights into the inner workings of single cells, we still lack an understanding of plasticity in development: How does one embryo differ from another and how can we describe the "average", stereotypic embryo?

To address this long-standing multi-disciplinary challenge, we propose to develop an entirely novel microscopy hard- and software platform to systematically image and analyze embryos in real time. We will design and assemble a fast and flexible multimodal light-sheet microscope (SPIM) with adaptive illumination and detection from multiple sides. A fundamentally new concept of this proposal is the ability to adaptively change the recording's spatial and temporal resolution during the experiment: The microscope learns to acquire only the data of interest. Using a high-throughput sample feeder, many samples can be automatically pumped through the microscope and imaged within seconds for large-scale comparative developmental studies. Real-time processing will dramatically reduce the size of the data stream and thus, provide for the first time a platform to collect data from hundreds of samples. At the same time, by establishing a model for the observed embryo, we will integrate information from multiple samples to draw statistically relevant conclusions.

Our ground-breaking concept of smart microscopy speeds up the acquisition, reduces the amount of data and limits photo-toxicity. It enables us to address fundamental questions in embryonic development that are out of reach by traditional methods. Smart microscopy will open up a new field of research: systematic realtime developmental biology.
With an early termination after not even two years out of the total of five years of approved funding means that not all research aims will have been completed. However, since the project has already made excellent progress we are confident that the remaining time will allow us to complete three aims (aims 1, 2 and 5) and partially complete two aims (aims 3 and 6). Aim 4, which is dependent on the results from aims 1 to 3, was planned to be done towards the end of the project, and will not be completed.

The design of the fast and flexible light sheet microscope (aim 1) has made good progress and will be completed in the proposed remaining time of the project. A prototype has been built and the fast and adaptive illumination scheme has been tested meanwhile on a separate setup. We are currently preparing the two publications. The two concepts will then be fused into a single instrument.

Different smart acquisition concepts are currently being theoretically tested on existing data (aim 2) and will now be tested on biological data acquired in real time. The remaining time will allow us to evaluate and enhance the performance of the algorithms and present the world-wide first “smart microscope”. Applications to be tested include the smart acquisition of the cardio-vascular system and early cell divisions in zebrafish.

The algorithms developed in aim 2 will need to be implemented in a real-time environment to provide the targeted performance in aim 3. Due to the time constraints, we will implement all algorithms on CPU and will not test other architectures for even better performance.

A prototype of a high-throughput sample feeder (aim 5) has been developed and is currently been tested for a variety of applications. In the remaining time of the project the system will be benchmarked and implemented in the four-lens microscope (aim 1) and the smart acquisition scheme (aim 2) will be used to control the flow and sample delivery.

After the first demonstrations of a multimodal SPIM/OPT system (Bassi et al, Development, 2015) we are now exploring the spectral response of transmission images in live zebrafish. We hope to gain valuable information of the tissue under observation from the respective spectral transmission. While the implementation of these concepts will be successfully tested and implemented on stand-alone systems, we do not foresee an integration into the four-lens
microscope as originally planned for the five-year project.