Spatial ‘Omics Scientist

About This Role

This role involves co-developing next-generation technology for high-throughput connectomic imaging within E11 Bio, focusing on molecular barcodes. This scientist will design experiments, analyze image data, and contribute to open scientific results for public benefit. Join a collaborative and interdisciplinary team at a non-profit research organization.

Responsibilities

• Develop proteomics methods for highly multiplexed detection of antibodies in expansion microscopy using combinatorial imaging
• Develop robust signal amplification methods for detection of protein-based cellular barcodes and molecular markers at proteomic scale in swellable hydrogels
• Design probe sets and combinatorial imaging experiments (e.g., in situ sequencing, MERFISH) compatible with expansion microscopy to detect cell barcodes in brain tissue
• Integrate and apply automatic liquid handling and automatic fluorescence imaging methods in a robust and reproducible pipeline
• Process and analyze multiplexed image volumes, including stitching and registration across imaging cycles, and feature detection, decoding and classification
• Work closely with experimental and computational scientists at E11 and through external partnerships to collaboratively design experiments, analyze experimental data, and interpret results
• Maintain excellent laboratory notebook practices, prepare reports and manuscripts, and present results internally and externally, and source new techniques from the scientific community

Requirements

• PhD in biology or related field, or equivalent experience
• Experience with 3D spatial transcriptomics and/or spatial proteomics
• Extensive experience with spatial methods/protocol development, with emphasis on DNA-based readout such as HCR or RCA
• Experience with fluorescence microscope modalities, including spinning-disc confocal microscopy
• Experience with molecular biology laboratory techniques (e.g., cell/tissue culture, molecular cloning, qPCR, immunohistochemistry)

Qualifications

• PhD in biology (e.g. biophysics, bioengineering, molecular biology) or a related field in science and/or engineering, or equivalent working experience and track record
• 0-6 years of experience post-PhD, or equivalent industry track record

Nice to Have

• Experience with expansion microscopy and/or hydrogel embedding
• Experience with fluidics for multiplexing, microfluidics, and automation
• Experience with computational image analysis methods for combinatorial imaging

Skills

* Required skills

Benefits