AI Biologist – SpatialBench

This is a fully remote position, open to applicants in California.

📋 Description

• Develop testing tasks to evaluate the capabilities of AI agents in executing real spatial transcriptomics projects.

• Choose tissue-image alignment methods and analyze their subsequent impacts.

• Create multi-stage assignments inspired by actual published studies.

• Assess whether AI agents comprehend the reasoning behind various workflow decisions.

• Construct benchmarks with multiple checkpoints.

• Examine the management of registration failures.

• Assess segmentation thresholds and deconvolution assumptions in tissues exhibiting diverse morphologies.

• Collaborate with the Biosurveillance team at the intersection of AI and biology.

⛳️ Requirements

• Familiarity with spatial transcriptomics workflows.

• Understanding of how tissue alignment and background removal influence segmentation quality.

• Knowledge regarding nucleus-level versus spot-level segmentation and deconvolution.

• Proficiency in RCTD, Tangram, SPOTlight, and STRIDE.

• Awareness of the trade-offs between Visium, MERFISH, and Xenium platforms.

• Capability to determine when to deconvolve spots versus segment first.

• Comprehension of how cell density and tissue morphology limit method selection.

• Ability to learn and utilize Baysor, STdeconvolve, giotto, Squidpy, and image-processing pipelines.

• Competence in building multi-checkpoint benchmarks.

• Skill in managing registration failures, justifying segmentation thresholds, and defending deconvolution assumptions.

• 1099 or W8-BEN contract setup.

• Availability for 40 hours per week.

• OPT visa holders only; not eligible for STEM Extension.

🏝️ Benefits

• 2-4 week paid onboarding period.

• Full on-target earnings from day one.

• Two complimentary meals daily.

• Unlimited snacks available.

• Company outings held most months.

• Team retreats.

• Monthly parking provided based on availability.

• Truly flexible work schedules.

• Waterfront office located near Oracle Park / China Basin.

• Opportunities for advancement to more senior roles for candidates with demonstrated management expertise.