AI Biologist - Microscopy

Position Title: AI Biologist - Microscopy Work Location: San Francisco or Remote Assignment Duration: FTE role Work Arrangement: San Francisco or RemotePosition Summary: Our organization builds rigorous scientific benchmarks (benchmarks.bio) for AI agents across biology. We work with frontier labs and pharma to measure whether agents can handle real biological workflows: the messy, multi-layer reasoning that matters in the field.Background & Context: We’re seeking an AI Biologist to join our Microscopy team, pushing what AI can achieve in biological imaging.Key Responsibilities:Define what expert reasoning looks like for an imaging question, and write gold-standard answers with the rationale an experienced microscopist or pathologist would defendDesign realistic scenarios across the imaging workflow: sample prep, staining, acquisition, preprocessing, segmentation, quantification, and interpretationCurate image datasets across modalities: immunofluorescence, confocal and live-cell, electron microscopy, histology and histopathology, and high-content screeningBuild analysis pipelines in Python, including deep-learning segmentation, that produce verifiable ground truthPartner with software engineers to turn your judgment into new workflowsTest whether agents distinguish true signal from artifact, such as bleed-through, uneven illumination, fixation damage, out-of-focus planes, or segmentation failureAdjudicate ambiguous images: decide what the data supports, where reasonable experts would disagree, and which additional stain, image, or experiment would settle the callTest whether agents choose the right imaging modality, resolution, and unit of analysis for the questionInterrogate agent reasoning step by step, and challenge conclusions that sound right but would not survive pathologist review or lab meetingPinpoint where agents go wrong: why a step fails, what an expert would do instead, and what evidence would change the callScore agent confidence, rewarding explicit uncertainty over overconfident calls on ambiguous imagesQualification & Experience:PhD in cell biology, bioimage analysis, pathology, or a related field; or an MD with pathology trainingSenior, hands-on imaging experience: you have looked at thousands of samples and know what normal and abnormal look likeDirect experience with image segmentation tools such as CellProfiler, Cellpose, StarDist, QuPath, ilastik, napari, or FijiDeep expertise in at least one area (bioimage analysis, cell biology, or histopathology) and working fluency across the othersStrong command of experimental design, image quantification, and statisticsAI-ready from day one: daily use of Claude, Cursor, or similar agents, with the judgment to spot where model reasoning is technically correct but scientifically unsoundConfidence to overrule an AI agent when the evidence demands it, and the openness to update when shown wrongAbility to calibrate confidence and communicate uncertainty rather than defaulting to binary callsBonus: electron microscopy, pathology, or pharmacology experience (e.g., pharmacodynamic or drug-uptake imaging assays)Bonus: familiarity with public resources such as the Image Data Resource (IDR), BioImage Archive, Human Protein Atlas, Cell Painting Gallery, or TCGA whole-slide imagesApplicant Notices & DisclaimersFor information on benefits, equal opportunity employment, and location-specific applicant notices, click here