Pursuit of connectomics: Looking for a needle in a haystack

Abstract: A major challenge in neuroscience is to relate the structure of neurons to their function. More than a century ago, Santiago Ramón y Cajal found that neurons are polarized cells with dendrites and axons, the input and output ends of neurons respectively. We now know that a neuron's structure is intimately related to its function. In this talk, I will discuss our recent advances to develop an efficient pipeline to map the complete axonal projections of individual neurons across the entire mouse brain. This is a challenging task because on the one hand axons are tiny, with diameters of less than 100 nanometers; tracing axons thus requires resolution and sensitivity at the cutting edge of what is possible with optical microscopy. On the other hand, axonal arbors are huge; individual axons of projection neurons can traverse tens of centimeters across the mouse brain before reaching their targets that makes generating morphology from large scale data manually a time consuming process. To tackle this challenge, we have developed various automated computational tools for detection, stitching, segmentation and visualization of neuronal process for massive volumes of data and generated more than two hundred whole neuronal reconstructions that will provide new insights into neuroscience.

Bio: Erhan Baş received his PhD in Electrical and Computer Engineering from Northeastern University, Boston in 2011. He joined the Mouselight team at Janelia Research Campus (JRC) of HHMI as a computer scientist in 2015. At JRC, he is interested in large scale image analysis techniques for neuronal morphology analysis. Before joining to JRC, he was with the computer vision lab at GE Global Research in Niskayuna, NY, where he led a team of material and computer scientists working on industrial inspection technologies and he was an adjunct professor at Rensselaer Polytechnic University (RPI), Troy, NY where he taught Biological Image Analysis course. His general research interests include machine vision and statistical pattern recognition with various applications in biomedical and industrial image processing. He is one of the five Diadem challenge finalists and he serves as a member of IEEE Bio Imaging and Signal Processing Technical Committee, where he has been serving as an organizing committee member and area chair of ICIP 2015 and ISBI 2015/2018.