Expansion Microscope Image Reconstruction by Monte Carlo Method

Chi-Tin Shih^1,2*, Chunpin Chiang²

¹Department of Applied Physics, Tunghai University, Taichung, Taiwan
²Brain Research Center, National Tsing-Hua University, Hsinchu, Taiwan

* Presenter:Chi-Tin Shih, email:ctshih@thu.edu.tw

The expansion microscopy (ExM) technique allows nanoscale imaging of brain tissues by optical microscopes, which can identify the synaptic connection between neurons. However, depth and field of view are limited under such high resolution. To obtain the nanoscale images of the Drosophila (fruitfly) brain by ExM, the sampe has to be divided into smaller cubes and scanned one by one sequentially, and then sub-images of the cubes have to be stitched together to reconstruct the whole brain image. Besides the correct position of the cubes, we also need to estimate the expansion ratio for each cube because the sampe expansion is still going on during the imaging process, which makes the reconstructions more difficult. In the present study, we use Monte-Carlo method to find the position and expansion ratio of each cube to reconstruct the optimal whole brain image of the fruitfly. The technique will be very helpful for the construction of the structural and functional connectome of brains.

Keywords: connectome, expansion microscopy, brain imaging, Monte-Carlo, simulated annealing