Lab Administration Coordinator III

The Computational Microscopy Imaging Lab (CMI Lab) led by Dr. Pinaki Sarder in the Department of Medicine at the University of Florida is seeking a highly experienced data scientists with precise understanding of the concept of timely deliverable for a high-risk, high-reward project funded by Human Biomolecular Atlas Project (HuBMAP) consortium. The project entails digital histology and multi-channel CODEX fluorescence images, cell segmentation, multi-dimensional feature extraction from cells, cell clustering, cell type annotation, and error connection.

HuBMAP is a visionary, premier multi-year project by NIH involving investigators across the country from various different labs with knowledge spanning in organ systems, cutting edge molecular imaging and assays, data science, systems engineering, data visualization and more. For detailed information see,

Successful candidate will be fast learner and have background in data science, imaging, image analysis, machine learning, computer coding, and basic biology of various human organ systems. The candidate will work directly with a dedicated PhD student who is driving the project, and national and international experts in the associated area, in a fast, rapidly evolving project.

Data science support 50%

• Gather histology and CODEX data of various organ systems in standard format from various experimental collaborators across the consortium
• Necessary QA/QC of the data
• Run existing pipelines established in the lab for cell type ground truth annotations
• Run existing machine learning models established in the lab for cell type predictions from histology images. This part needs independent working skill of the candidate to make necessary changes in the available scripts to make it adoptable to the image, data, and cell type abundance in the data
• Ability to review the results either by them or via reaching out to collaborators, correct error, and rerun the pipeline via refining the classification problem to be solved. This part of the work requires knowledge in cell systems morphometry and molecular information of various organ systems
• Finalize the pipelines for various organ systems and then cross organ training and testing for common cell types
• Refine the codes and models in generalized, standard, and trustable form for others to use.
• Lead a usability study for evaluating the trained model within or outside the consortium in data that was not seen by the model
• Follow best software engineering practices, maintain documentations, and ensure FAIR execution of the project and software

Meeting engagement across the consortium & internal team members 30%

• Discuss with various stakeholders within and outside the consortium for feedback and use their inputs for refining the proposed model.
• Work closely with the project lead (a PhD student), the PI, and other investigators from the project as well as other scientists from the PI s lab.

Report & manuscript writing 10%

• Maintain regular weekly report on the progress, as well as document technical challenges
• Prepare manuscripts as needed

Other duties, 10%

• Assist in organizing project data, files, documentation
• Provide tutorial on the project if/ as needed
• Assume the roles of project managers in the project meetings
• Other duties as assigned.