3D image analysis using AI, XR, and spatial computing

Conventional histopathology techniques, which diagnose structural and molecular changes by examining thin tissue sections under a microscope, have been widely used for over a century. However, the 2D images obtained from thin sections of tissues only provide a single plane of view and do not capture the 3D structure of the tissue, limiting its ability to represent the complex structures of tissues and organs. Consequently, crucial information about the spatial relationships between different cells, tissue structures and drug targets can be lost¹.

To address these limitations, 3D imaging techniques have been developed to visualize the entire 3D structure of tissues and organs. Confocal microscopy or light-sheet microscopy captures optical section images of the entire sample enabling a better understanding of the abnormalities caused by drug toxicity or diseases in 3D².

We envision that the integration of 3D imaging and AI into extended reality and spatial computing has the potential to revolutionize 3D histopathology image analysis³. Our lab has already established expertise in 3D histopathology, employing techniques such as light-sheet microscopy, laser scanning confocal microscopy and expansion microscopy to examine organs, cells, and subcellular organelles across scales ranging from millimeters to nanometers. We have also been using AI tools for digital image analysis of 2D images⁴.

To expand our capabilities further, we aim, as part of this opnMe call, to develop AI-powered 3D image analysis utilizing extended reality and spatial computing. This approach will enable us to leverage the advantages of both AI and spatial computing to gain deeper insights into the complex 3D structures and spatial relationships within tissues and organs.

As a summary, how would you employ artificial intelligence, extended reality, and spatial computing to analyze 3D images of tissues and organs, with the aim of enhancing our understanding of morphological and molecular alterations induced by diseases and drug toxicity?

We are inviting proposals that provide detailed plans for a well-structured project, which should be completed within a 3-year timeframe. The primary objective of the project is to develop a platform for 3D biomedical image analysis utilizing artificial intelligence, extended reality, and spatial computing. The platform should offer a user-friendly workflow through (semi)automated data processing and a collaborative workspace.

• Hardware (microscope, computer, headset) development
• Sample preparation method development
• 3D imaging method development
• Pathological diagnosis

As a winner of this call, you will have the unique opportunity to pursue your own submitted research project as a fully resourced PostDoc project under the guidance of mentors in the department of Nonclinical Drug Safety at Boehringer Ingelheim located in Biberach/Riss, Germany. You will obtain a position for up to 3 years* with Boehringer Ingelheim within a cross-functional, international team of world-class toxicologists, pathologists, digital image analysts, and AI scientists working on drug safety. [*The offered position initially covers a duration of 24 months with an option for extension by another 12 months.]

At Boehringer Ingelheim, you will have access to a fully equipped laboratory in a state-of-the-art research facility including access to all relevant tools (e.g., Light-sheet microscope, laser scanning confocal microscope, high power computing system) and technologies. You will benefit from mentoring through our internal experts, have the chance to attend international conferences, and to publish your results in high-ranking journals. You will be part of the vibrant PostDoc community at Boehringer Ingelheim in Biberach with manifold opportunities for scientific, cross-functional exchanges for your personal development. You will have the opportunity to learn the process and challenges of drug discovery and development from the inside, including additional training and mentoring programs.

In addition, benefit from the rich packages for employee benefit. Our most important asset in achieving our global vision is our people. We prioritize your growth, investing in our people through mentoring, coaching, skill-building, leadership development, and academic support. Our infrastructure promotes wellness with sports groups, health counseling, onsite medical services, and regular check-ups. Achieve work-life balance with flexible work hours, remote working, childcare support, counseling, and convenient amenities. We ensure financial health with employer loans, private insurances, access to discounts, and a company pension scheme. Benefit also from our excellent and healthy on-site catering and the opportunity for take away meals. We offer relocation support and interim accommodation to make joining us easy.

• PhD or equivalent degree in Computer Science, Physics, Life Sciences, or related field.
• Strong background in developing AI algorithms for microscopy image analysis.
• Proficiency in computer programming languages.
• Knowledge of extended technologies in biomedical imaging.
• Practical experience in histopathology techniques.
• Extensive knowledge of fluorescence microscopy and familiarity with 3D imaging techniques (e.g., light-sheet microscopy).
• Strong problem-solving skills and ability to work independently, proactively, and collaboratively.
• Track record of independent research as exemplified through publications or patents.
• Very good oral communication and presentation skills as well as the ability to work in multidisciplinary teams in a matrix environment.
• Fluent language skills in English are mandatory, German language skills is a plus.

Please use our PostDoc grant application template to provide a 4-5 page non-confidential proposal (available for download here). Please complement with your CV, publication list, and recommendation letters.

If confidential data exists that would strengthen the proposal, please indicate that information is available to share under a Confidential Disclosure Agreement (CDA). If we find the non-confidential concept proposal sufficiently interesting, we will execute a CDA for confidential discussions.

We can only accept research proposals if they arrive by the submission deadline on June 12, 2024, 11.59 pm PST.

All incoming applications accompanied by a research plan will be evaluated by a scientific jury, and, upon selection, you as the winner will have the opportunity to pursue your research project as defined by yourself as part of your PostDoc studies at Boehringer Ingelheim. An attractive package including salary, expenses, and additional company benefits will apply.

We can only accept research proposals if they arrive by the submission deadline on June 12, 2024, 11.59 pm PST.