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Computational Spatial Transcriptomics Jobs (NOW HIRING)

Ionis

Director, Computational Biology

Carlsbad, CA · On-site +1

... spatial transcriptomics, proteomics, metabolomics, ChIP-seq and similar, long read RNA-seq, small ... computational partners) and translating complex computational findings into clear, actionable ...

Uw

Research Scientist/Engineer 3

Seattle, WA

This position is engaged in the field of Spatial transcriptomics and bioinformatics. This position ... Bachelor's degree in Bioinformatics, Computational Biology, Biostatistics, Data Science or a ...

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Computational Spatial Transcriptomics information

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How much do computational spatial transcriptomics jobs pay per hour?

As of Jun 18, 2026, the average hourly pay for computational spatial transcriptomics in the United States is $54.93, according to ZipRecruiter salary data. Most workers in this role earn between $46.88 and $73.56 per hour, depending on experience, location, and employer.

What are some typical challenges faced when working in computational spatial transcriptomics, and how can new team members prepare for them?

Professionals in computational spatial transcriptomics often encounter challenges related to handling and analyzing large, complex datasets that combine spatial and gene expression information. Integrating data from different technologies and ensuring data quality can be demanding, requiring strong programming skills and familiarity with bioinformatics pipelines. New team members can prepare by strengthening their skills in statistical analysis, programming languages like Python or R, and staying updated on the latest spatial transcriptomics techniques. Collaborating closely with experimental biologists and data scientists is also key to overcoming these challenges and driving successful research outcomes.

What is the difference between Computational Spatial Transcriptomics vs Computational Biologist?

AspectComputational Spatial TranscriptomicsComputational Biologist
Required CredentialsAdvanced degrees in bioinformatics, computational biology, or related fields; experience with spatial data analysisTypically a PhD or Master's in biology, bioinformatics, or related disciplines; strong programming skills
Work EnvironmentResearch labs, biotech companies, academic institutions focusing on spatial genomicsResearch institutions, biotech firms, academia working on biological data analysis
Industry UsageSpecialized in spatial transcriptomics techniques and data interpretationBroad biological data analysis across various fields

Computational Spatial Transcriptomics focuses on analyzing spatial gene expression data within tissues, requiring specialized skills in spatial data processing. In contrast, Computational Biologists work on a wider range of biological data types. While both roles involve bioinformatics expertise, the former emphasizes spatial data analysis techniques specific to transcriptomics.

What is computational spatial transcriptomics?

Computational spatial transcriptomics is a field that combines advanced computational methods with spatial transcriptomics, a technique that measures gene expression within the physical context of tissue samples. It involves processing and analyzing large datasets to map where specific genes are active within tissues, helping researchers understand how cells interact and function in their native environments. This approach is crucial for studies in developmental biology, cancer research, and neuroscience, as it provides insights into cellular organization and tissue architecture. Computational tools help extract meaningful patterns from complex data, enabling discoveries that were previously impossible with traditional methods.

What are the key skills and qualifications needed to thrive as a Computational Spatial Transcriptomics Scientist, and why are they important?

To excel in Computational Spatial Transcriptomics, you need a strong background in bioinformatics, genomics, and statistical data analysis, typically supported by advanced degrees in computational biology or related fields. Familiarity with programming languages (such as R and Python), spatial transcriptomics platforms (like 10x Genomics Visium), and high-throughput sequencing data analysis tools is essential. Strong problem-solving skills, attention to detail, and effective communication are crucial soft skills for interpreting complex datasets and collaborating with multidisciplinary teams. These competencies ensure accurate data interpretation, innovative research, and successful integration of spatial transcriptomics insights into biological and clinical applications.
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Computational Spatial Transcriptomics jobs near you
Infographic showing various Computational Spatial Transcriptomics job openings in the United States as of June 2026, with employment types broken down into 69% Full Time, 30% Part Time, and 1% Contract. Highlights an 94% Physical, 1% Hybrid, and 5% Remote job distribution, with an average salary of $114,249 per year, or $54.9 per hour.
Histology Core Facility Director

Histology Core Facility Director

Cold Spring Harbor Laboratory

Cold Spring Harbor, NY • On-site

$100K - $125K/yr

Full-time

Medical, Retirement, PTO

Posted 8 days ago

Job description

Salary: $100,000.00 - $125,000.00 Annually
Location : 500 Sunnyside Blvd, Woodbury - Genome Center
Job Type: Full Time
Job Number: 2198
Process Level: Scientific Laboratory
Opening Date: 06/10/2026
Position Description
Cold Spring Harbor Laboratory is seeking an experienced and highly collaborative Ph.D. or M.D. scientist for an immediate opening as Director of the Histology Core Facility. The successful candidate will provide strategic, operational, and scientific leadership for a busy, growing histology core supporting cutting-edge basic and translational research programs in areas such as cancer biology, neuroscience, and spatial biology. The Histology Core Facility is part of CSHL's NCI Cancer Center Animal and Tissue Imaging Shared Resource, but provides services to the entire CSHL research community.
This position requires a strong leader and manager with demonstrated experience overseeing personnel, laboratory operations, workflow optimization, and customer engagement in a research core environment. In addition to ensuring outstanding day-to-day operations, the Director will be expected to develop and execute a forward-looking vision for the future growth of the Histology Core, including expansion of capabilities in digital pathology, advanced image analysis, multiplex imaging, and integration with spatial biology workflows across the institution.
The successful candidate will join a vibrant, collaborative scientific community at Cold Spring Harbor Laboratory and work closely with investigators and institutional core facilities, including the Single Cell Biology Core, to develop and implement emerging technologies in areas such as spatial transcriptomics, multiplex imaging, quantitative pathology, and computational tissue analysis. The Histology Core currently includes four histology technicians, including several highly experienced senior staff members with extensive core facility expertise.
Position Responsibilities
The Director of the Histology Core Facility will oversee all day-to-day operations of the core facility, including personnel management, project coordination, quality control, budgeting input, equipment oversight, and customer interactions, as well as optimizing existing workflows for improved throughput and efficiency.
In addition to operational leadership, the Director will help shape the core's strategic scientific direction by identifying, developing, and implementing emerging technologies and analytical approaches that enhance institutional research capabilities.
Key responsibilities:
  • Provide leadership, supervision, mentoring, and professional development for core facility staff
  • Manage and improve operational workflows, turnaround times, communication, and project tracking systems
  • Develop and execute a strategic vision for the growth and modernization of the Histology Core
  • Expand institutional capabilities in digital pathology, whole-slide imaging, immunofluorescence (IF), and immunohistochemistry (IHC), and quantitative image analysis
  • Build integrated workflows with the Single Cell Biology Core to support spatial transcriptomics and spatial biology applications
  • Consult with investigators on experimental design, tissue processing strategies, histological methods, and image analysis approaches
  • Oversee and participate in experimental workflows, including tissue processing, embedding, sectioning, staining, IF/IHC, and in situ hybridization
  • Develop, validate, and implement new histology, imaging, and analytical workflows
  • Advise on acquisition, optimization, maintenance, and utilization of instrumentation and core technologies
  • Support digital pathology and image analysis workflows, including whole-slide imaging and quantitative image analysis
  • Collaborate with institutional investigators and other core facilities on emerging technologies, including multiplex and cyclic immunofluorescence, spatial transcriptomics, and computational pathology approaches
  • Support institutional grant applications and reporting requirements, including renewals of the Cancer Center Support Grant and progress reports
  • Participate in all Cancer Center activities, including advisory boards and grant reviews, as requested by the Cancer Center leadership

Position Requirements
EDUCATION: An advanced degree in the biological sciences (PhD or MD) is preferred; candidates with a master's or bachelor's degree and extensive histology experience will also be considered.
SKILLS/EXPERIENCE:
  • At least 3 years of experience working in a histology, pathology, or related academic core facility
  • Demonstrated experience helping develop or expand core facility technologies, workflows, or scientific capabilities
  • Experience managing or supervising technical staff within a shared-resource or service-oriented environment
  • Expertise in digital pathology, whole-slide imaging, and/or quantitative image analysis
  • Experience with image analysis platforms such as Visiopharm, HALO, QuPath, or related software
  • Experience with advanced multiplex imaging approaches, including cyclic immunofluorescence and spatial biology workflows
  • Computational and analytical experience related to image analysis, including cell phenotyping, spatial/neighborhood analysis, and high-dimensional imaging datasets
  • Experience integrating histology and imaging workflows with spatial transcriptomics or single-cell technologies
  • Experience evaluating, implementing, and optimizing new instrumentation and technologies

Supplemental Information
How to Apply:If you are a collaborative and forward-thinking histology leader with expertise in laboratory operations, personnel development, and quality assurance, and are committed to supporting cutting-edge research, we encourage you to apply. Please submit an online application here: Position ID 2198
EnvironmentCold Spring Harbor Laboratory is a world-renowned biomedical research institution in New York. It has shaped contemporary biomedical research and is the home of eight Nobel Prize laureates. Cold Spring Harbor Laboratory provides a highly dynamic and interactive research environment and also a unique opportunity of timely exposure to advances in various biomedical research fields and of interaction with a broad range of researchers from all over the world through its renowned Meetings and Courses program. We believe that science is for everyone and our researchers have a wide variety of backgrounds.
Compensation and Benefits: Our employees are compensated in many ways for their contributions to our mission, including competitive pay, exceptional health benefits, retirement plans, time off, and a range of recognition and wellness programs. Visit our CSHL sites to learn more. The salary range for this role is $100,000-125,000 per annum. The salary range and/or hourly rate listed is a good faith determination of potential base compensation that may be offered to a successful applicant for this position at the time of this job advertisement and may be modified in the future. When determining a base salary and/or rate, several factors may be considered as applicable (e.g., years of relevant experience, education, credentials, and internal equity).
CSHL is an EO Employer. All qualified applicants will receive consideration for employment and will not be discriminated against on the basis of race, color, religion, sex, sexual orientation, gender identity, national origin, age, disability or protected veteran status. VEVRAA Federal Contractor
Our employees are compensated in many ways for their contributions to our mission, including competitive pay, exceptional health benefits, retirement plans, paid time off, a Wellness Center and access to an affordable and licensed on-site childcare center. Visit our site to learn more.

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