New York, New York, United States
Research scientist specialized in image processing and automation in the cryo-electron microscopy and deep-learning histopathology fields. Applied organization skills toward consistently achieving objectives and deadlines with proven successes in managing projects from inception through completion.
Image processing specialist * in bio-medical images (Applied Bioinformatics Labs): - Image and Electronic Health Record data analysis with supervised and unsupervised convolutional neural networks (whole slide histopathology images of lung cancer, melanoma, osteosarcoma, preclinical studies, auto-immune diseases, etc) for disease classification, survival prediction, biomarkers identification or response to treatment prediction. - Coordinate over 10 projects with collaborators; assist undergrad/PhD/Postdoc fellows with their projects * in cryo-EM/ET (2017-2024; Bhabha+Ekiert labs): - 3D reconstruction of proteins from cryo-EM/ET using single particles and tomography tools (bacterial membrane proteins, microsporidia parasites, motor proteins...) - Use, test and teach image processing tools (Relion, CryoSparc, Dynamo) for 3D reconstruction, maintain pipelines and coordinate with HPC teams - Assist PhD/Postdoc fellows & collaborators with image acquisition and processing
Analysis of membrane proteins (Stokes' Lab): - Developed Matlab and Python programs to assist data analysis or image processing - Solved the structure of membrane proteins by cryo electron microscopy (Titan Krios) - Developed new techniques to validate helical crystal indexing - Designed and supervised 2D-crystallization experiments
Context: High-throughput screening of protein 2D crystals as part of the TEMIMPS research consortium (temimps.nysbc.org/), funded by the NIH PSI:Biology program. Main contributions: - Planned and supervised crystallization screening projects (over 300 experiments for 57 membrane protein targets) - Coordinated the projects with collaborators from various American universities - Developed and maintained a robotic tool chain for high-throughput screening, including an automated JEOL 1230 microscope (throughput improved by a factor of 4.8) - Conceived programs (Matlab and Python) to assist data analysis and image processing - Increased the crystallization success rate by designing new and more efficient screening strategies - Conceived a database to facilitate the design of new screens and better understand the crystallization process (data mining and statistical analysis) - Analyzed the output of 2D crystallization experiments and wrote summary reports - Solved the structure of the zinc transporter YiiP protein from helical crystals using various image processing tools
Developed image processing algorithms for the automatic screening of various biological samples (using Matlab).
Context of the research: to achieve the high-throughput screening of biological samples (2D crystals of membrane proteins) as part of the HT-3DEM European project (High Throughput - Three Dimensional Electron Microscopy) Main contributions: - Created an Matlab Image Processing Toolbox for the automatic control of a microscope and the characterization of biological samples - Improved the speed of the screening process by integrating those algorithms into a Tecnai F20 microscope (extensive collaboration with the University of Basel and FEI company). - Participated in writing progress reports with milestones Teaching at the University of Technology (2009-2010): - Industrial data processing (Microprocessor control) - Supervision (Human-computer interactions) - Internship coordinator Teaching at the National School of Engineers of South Alsace (ENSISA): - Programmable Logic Controller (Ladder, Grafcet and Logic Blocks programming) - VHDL Programming (Electronic systems simulation)