Research Assistant Professor - Brain Circuit Imaging and Atlas Mapping

Research Assistant Professor - Brain Circuit Imaging and Atlas Mapping Category: Science Subscribe: New Job Alerts RSS Job Feed Department: Biological Sciences Locations: El Paso, TX Posted: May 27, 2026 Closes: Open Until Filled Type: Full-time Ref. No.: RREP-26-018 Position ID: 200930 Share About The University of Texas at El Paso: The University of Texas at El Paso (UTEP) is a Carnegie R1, equal opportunity, and community engaged university at the heart of the U.S.-Mexico border region that is increasing access to excellent higher education. We advance discovery of public value and positively impact the health, culture, education and economy of the community we serve. UTEP enrolls more than 25,000 students, 85% of whom are Hispanic and half of whom are the first in their families to attend college. UTEP offers 171 bachelor's, master's and doctoral degree programs at the only open-access, top-tier research university in America. Located at the westernmost tip of Texas, El Paso is set against the backdrop of the Franklin Mountains and the Chihuahuan Desert in one of the largest binational communities in the world. A family-oriented community that is one of the safest large cities in the U.S., the cost of living in El Paso is very reasonable with an average home value of $224,000 in 2025, and Texas has no income tax. The region's rich culture includes a vibrant street art and mural scene, art galleries, a new children's museum and science center, the state's longest-running symphony orchestra and a full schedule of seasonal events and festivals. Sports fans will enjoy Division I college athletics, Triple-A baseball affiliate the El Paso Chihuahuas and professional soccer team El Paso Locomotive FC, and outdoor enthusiasts will be drawn to year-round hiking, mountain biking and rock climbing in nearby state and national parks. About the Department of Biological Sciences The Department of Biological Sciences offers two Ph.D. tracks (Bioscience and Ecology and Evolutionary Biology) and has over 100 graduate students and over 2,000 undergraduate majors, including over 150 neuroscience majors. Biological sciences faculty maintain strong collaborative and programmatic ties with several other departments, including Psychology, Pharmacy, Physics (including imaging faculty), Chemistry, and Computer Science. The department hosts a vibrant neuroscience research community, with an active program in mesoscale chemoarchitectural mapping of the rat brain spanning experimental neuroanatomy, whole-brain imaging, atlas-based data integration, and computational tools that preserve the spatial provenance of molecular and physiological datasets. The cluster hire described in this announcement extends these strengths toward an integrated research program on the neural circuitry of craving, reward, and addiction. The pipeline begins with rat drug- and food-reward studies run by cluster co-PIs in Psychology and Pharmacy, who supply the brain samples for downstream imaging and atlas mapping. Imaging is anchored by the NIH-funded Imaging & Behavioral Neuroscience (IBN) Core Facility - whole-brain 3-D microscopic imaging at the microcircuit level, with light-sheet microscopy as a core capability. UTEP's Border Biomedical Research Center (BBRC) serves as a strategic institutional partner and operates its own imaging core; shared campus high-performance computing resources support volumetric image rendering, large-dataset processing, and 3-D visualization at the scale whole-brain microscopy demands. The work is supported by multiple active federal awards. Job Description: 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. The position is one of four in a coordinated cluster hire - alongside colleagues in behavioral neuroscience, machine learning and AI, and research software engineering - studying the brain circuits underlying craving, reward, and addiction. Two methodological pillars anchor the role, equally weighted: mesoscale imaging acquisition and atlas mapping. Imaging covers light-sheet 3-D microscopy at UTEP's NIH-funded Imaging & Behavioral Neuroscience (IBN) Core Facility (with confocal, brightfield, and fluorescence as supporting modalities), tissue clearing, multi-channel acquisition, and visualization in Imaris, napari, and Fiji/ImageJ. Atlas mapping covers chemoarchitectural staining (immunostaining, Nissl/cytoarchitectonic analysis), plane-of-section analysis, mesoscale boundary determination, and integration into the Brain Maps 4.0 and Chemopleth 1.0 frameworks - the expert anatomical ground truth that anchors what the cluster's ML/AI hire automates downstream. The role pairs naturally with the IBN Core Facility and the Brain Mapping & Connectomics (BM&C) undergraduate teaching laboratory, settings for training students in both pillars and partnering directly with the cluster's ML/AI and research software engineering hires on pipeline handoff. The cluster's ML/AI work is built on what this role provides: image fidelity and anatomical judgment. Position 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. Coordinate 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. The cluster will support training in the complementary pillar during the appointment; candidates strong in either are encouraged to apply. 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. Inquiries-including the filing of a Formal Complaint or reporting an incident-about the application of Title IX may be referred to the Title IX Coordinator, who can be reached by phone at ..., by email at ... , or by mail at 500 W. University Ave., El Paso, TX, Kelly Hall, Room 312. For accommodation information for employees and applicants with disabilities, please contact UTEP's Equal Opportunity Office at ... . 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. Application Instructions: A complete application includes: Cover letter describing research interests, relevant experience, and fit with the position Curriculum vitae Statement of research (maximum of 2 pages) Names and contact information for three professional references Up to three representative publications, preprints, or software/data artifacts Review of applications will begin immediately and continue until the position is filled. Questions about the position may be directed to the search committee chair, Dr. Arshad M. Khan ( ... ). Frequently Asked Questions (FAQs) Powered by