Senior Bioinformatics Research Scientist- Bioimage analysis

Memphis, TN

About St. Jude Children's Research Hospital

The World’s Most Dedicated Never Give Up

There’s a reason St. Jude Children’s Research Hospital is recognized as a great place to work. Because at our world-class pediatric research hospital, every one of our professionals shares our commitment to make a difference in the lives of the children we serve. There’s a unique bond when you’re part of a team that gives their all to advance the treatments and cures of pediatric catastrophic diseases. The result is a collaborative, positive environment where everyone, regardless of their role, receives the resources, support and encouragement to advance and grow their careers and be the force behind the cures.

Senior Bioinformatics Research Scientist- Bioimage analysis

The NeuroImage Analysis core in the Department of Developmental Neurobiology (DNB) at St Jude Children’s Research Hospital is a team of computational scientists with a focus of turning image data into biological knowledge. We utilize computational tools at the cross-section of biology and cutting edge microscopy methods to understand how brains are built during development and how neurons function in the brain and malfunction in disease. We work closely with the NeuroImaging Laboratory (NIML), a facility that builds and implements advanced microscopy instrumentation, in order to ensure that the large and information-rich datasets produced by these systems are fully realized. This combinatorial approach allows novel imaging technology and analysis methods to grow simultaneously for mutual benefit.

 

We seek scientists who are passionate about expanding the interface between advanced microscopy instrumentation and computer vision and object detection.  Successful candidates will be creative-problem solvers from diverse backgrounds that can join with our highly collaborative culture at DNB to advance the understanding of the nervous system. This individual will have the opportunity to participate in open-source software development that will enable real-time autonomous decision-making in advanced microscopy platforms, and develop user interfaces to make these systems more accessible to biologists.

 

About St. Jude

There is a reason St. Jude Children’s Research Hospital is consistently ranked on Fortune Magazine’s “100 Best Places to Work For” list. At our world-class pediatric research hospital, every one of our professionals share our commitment to make a difference in the lives of the children we serve. There is a unique bond when you are part of a team that gives their all to advance the treatments and cures of pediatric catastrophic diseases. The result is a collaborative, positive environment where everyone, regardless of their role, receives the resources, support, and encouragement to advance and grow their careers.

 

About Memphis

This position is based in Memphis, TN; relocation assistance is available. Memphis is a family-friendly metropolitan area that more than a million residents call home. Memphis is recognized for its world-class music, food, and hospitality. Cost of living is one of our biggest attractions; in fact, Money listed Memphis as one of the least expensive cities in which to raise a child. Mild winters and beautiful green spaces make the city a magnet for outdoor enthusiasts – there are over 200 miles of bike-friendly lanes with more being added. Forbes recently named Memphis the 4th happiest city in which to work. Why live anywhere else?

  • Develop python-based tools like Napari that integrate with advanced microscope instrumentation in order to increase accessibility and accelerate adoption
  • Assist in developing and adapting image processing tools in the departmental and institutional compute ecosystems that make large advanced microscope datasets intelligible and viewable by biologists
  • Work with NIML staff to develop training materials, documentation, and SOPs for developed methods
  • The candidate will be proactive and initiate discussions with researchers and colleagues to understand the thrust of their domain science, identify algorithmic and software solutions relevant to ongoing scientific projects, and work collaboratively to develop software solutions where appropriate. The candidate will work closely with other data scientists to prioritize tasks
  • Excellent communication is a must
  • The successful candidate will have demonstrated effective oral and written communication skills and is expected to provide regular high-quality scientific reports of their work to scientists, collaborators, and team members. She/he is expected to maintain a positive working relationship with scientific staff and other groups
  • Minimum Requirement: Bachelor's degree with 7+ years of relevant post-degree work in bioinformatics, cheminformatics, statistics/computer science (with a background in biological sciences or chemistry).
  • Experience Exception: Master's degree with 5+ years of relevant post-degree experience (OR) PhD with 2+ years of relevant post-degree experience
  • Significant experience in at least one programming or scripting language and at least one statistical package, with R preferred
  • Experience with open source software development preferred
  • Experience in development of algorithms, statistical methods or scientific software preferred
  • Experience in next-generation sequence analysis or imaging analysis is preferred
  • Experience in working with high-throughput data sets in a highly competitive environment is preferred
  • Experience in working in a team project is preferred
  • Cross training in biological sciences (e.g. genomics, genetics, transcriptomics and epigenetics) preferred
  • 5+ years of hands-on experience with modern microscopy hardware or the development of specific analysis methods in close collaboration with imaging scientists preferred
  • Successful track record of using or developing analyses pipelines for SPIM instruments preferred
  • Experience with Napari and Napari plugin development preferred

  • Experience with large datasets in commonly used microscopy image formats (.tiff, .zarr) preferred

  • Proficiency and familiarity with Napari, demonstrated development of Napari plugins preferred

  • Exposure to deep learning frameworks and a willingness to learn about deep learning preferred 

  • Exposure to open-source bioimage management tools like OMERO is a preferred
  • Familiarity and proficiency with modern microscopy hardware systems preferred
  • Expertise in selective plane illumination (SPIM) methods preferred