Research Assistant Professor - Brain Circuit Imaging and Atlas Mapping

About the role

The Department of Biological Sciences at The University of Texas at El Paso (UTEP) is hiring a non-tenure-track Research Assistant Professor in Brain Circuit Imaging and Atlas Mapping.

Responsibilities

• Lead microscopy operations at the IBN Core Facility across light-sheet 3-D (primary) and conventional modalities (confocal, brightfield, fluorescence), including calibration, sample throughput, and acquisition planning.
• Develop and maintain tissue-handling, optical-clearing, and multi-channel acquisition protocols for the cluster's mesoscale mapping work.
• Cook up acquisition-time processing - stitching, intensity normalization, channel alignment, denoising, dataset curation ? to produce ML-ready datasets for downstream registration and segmentation.
• Anchor atlas mapping in the Brain Maps 4.0 and Chemopleth 1.0 frameworks, including chemoarchitectural staining strategy (immunostaining, Nissl/cytoarchitectonic analysis), plane-of-section analysis, and mesoscale boundary determination across the rat brain.
• Curate expert-mapped datasets that serve as ground truth for the cluster's ML/AI registration, segmentation, and annotation models, with documented chemoarchitectural and cytoarchitectonic conventions for reproducibility.
• Integrate mapped data into Brain Maps 4.0 and Chemopleth 1.0 (and analogous mesoscale standards), establishing and maintaining interoperability with EBRAINS and the BrainGlobe ecosystem.
• Collaborate with the cluster's ML/AI and research software engineering hires on pipeline handoff, making sure imaging outputs and atlas-mapped datasets meet downstream computational needs.
• Partner with the cluster's behavioral neuroscience hire to align imaging and atlas-mapping strategies with experimental designs, tract-tracing protocols, and behavioral phenotypes.
• Contribute to peer-reviewed publications and federal grant applications describing the cluster's imaging methods, expert-mapped datasets, and atlas-integrated outputs ? including the open-access digital atlas of brain reward circuits.
• Bring both pillars into the Brain Mapping & Connectomics (BM&C) undergraduate teaching laboratory ? imaging methods (microscopy, tissue handling, optical clearing) and atlas-mapping methods (chemoarchitecture, Nissl/cytoarchitectonic analysis, plane-of-section analysis, BM4.0/Chemopleth integration) ? and mentor trainees engaged in cluster projects.

Requirements

• Ph.D. in neuroscience, anatomy, cell biology, biomedical engineering, or a closely related field; or a Master's degree with substantial professional/industry experience in mesoscale brain imaging or atlas-based anatomical mapping.
• Strong expertise in at least one of the two methodological pillars below:
  • Mesoscale imaging acquisition - experience with whole-brain or large-volume rodent microscopy: light-sheet 3-D microscopy, conventional modalities (confocal, brightfield, fluorescence), tissue clearing, multi-channel imaging protocols, and visualization in Imaris, napari, or Fiji/ImageJ.
  • Atlas mapping - experience with expert anatomical mapping of the rodent brain: chemoarchitectural staining (immunostaining, Nissl/cytoarchitectonic analysis), plane-of-section analysis, mesoscale boundary determination, and integration into reference atlas frameworks (Brain Maps 4.0, Waxholm Space, Allen Reference Atlas, Swanson, Paxinos, or analogous mesoscale frameworks).
• Experience training or mentoring undergraduate or graduate students in laboratory neuroanatomy or microscopy methods.
• Willingness to develop expertise in the complementary methodological pillar through structured mentoring during the appointment.
• Ability to work in interdisciplinary teams, translating imaging and/or atlas-mapping requirements into downstream computational workflows.

Preferred Qualifications

• Hands-on experience with specific light-sheet microscopy systems (e.g., Zeiss Lightsheet, MesoSPIM, LaVision UltraMicroscope, or custom platforms) and optical clearing methods (e.g., iDISCO, CUBIC, CLARITY, or comparable).
• Familiarity with modern volumetric image data standards and large-image tooling (e.g., OME-Zarr, BigDataViewer, BigStitcher).
• Experience with serial-section reconstruction or other complementary whole-brain imaging modalities (e.g., confocal mosaic imaging, two-photon serial tomography).
• Postdoctoral or substantial graduate/industry research experience in comparative and/or systems neuroanatomy.
• Hands-on experience with antibody validation, titration, and chemoarchitectural marker selection for IHC studies in rodent brain tissue.
• Familiarity with rodent brain atlas frameworks beyond those used in the cluster (e.g., Waxholm Space, Allen Reference Atlas, Swanson, Paxinos, or analogous mesoscale frameworks) and atlas-integration software tools.
• Experience working in academic research-intensive environments, including core facility operations.
• Familiarity with rat stereotaxic surgery and neuroanatomical tract-tracing methods.
• Engagement with FAIR/open-science practices and shared neuroscience infrastructure (e.g., EBRAINS, NIH BRAIN Initiative resources, the BrainGlobe ecosystem).
• Track record of independent grant submissions or co-authored funded proposals related to brain imaging, neuroinformatics, neuroanatomy, or biomedical microscopy.

Additional Information

Appointment: Non-tenure-track Research Assistant Professor. Initial appointment is for 12 months, renewable contingent on performance and funding availability. The position can be renewed for a maximum of 3 years; renewal beyond 3 years will depend on the candidate's ability to secure extramural funding.

Salary: Commensurate with experience and qualifications. The salary will depend on the candidate's qualifications and experience and includes excellent fringe benefits.

Hiring decisions are based on budget approval.

In keeping with its access, excellence, and impact mission, The University of Texas at El Paso is committed to an open, diverse, and inclusive learning and working environment that honors the talents, respects the differences, and nurtures the growth and development of all. We seek to attract faculty and staff who share our commitment.

The University of Texas at El Paso is an Equal Opportunity Employer. The University does not discriminate on the basis of race, color, national origin, sex, religion, age, disability, genetic information, veteran status, or sexual orientation and gender in employment or the provision of services in accordance with state and federal law. Discrimination on the basis of sex includes an employee's or prospective employee's right to be free from sexual harassment under Title IX of the Higher Education Amendments of 1972.

To the extent that this position involves research, work, or access to critical infrastructure as referenced in Executive Order GA-48, being hired for and continuing to be employed in this position requires the ability to maintain the security or integrity of the infrastructure.