Scientist – Image Analysis

Job Description

The role

The successful candidate will work closely with the R&D team driving the development and optimization of image analysis modules for translating Nanopixel™ probed molecules into quantitative biological information. You will handle the raw output from different readers (such as fluorescence microscopes and high content imaging systems) to ensure precise and accurate translation to numerical data generated by APLEX Bio’s hpPCR assays. The role involves a keen attention to detail in a dynamic and interdisciplinary environment supporting ongoing and emerging applications of hpPCR. Your daily activities will contribute to a wide variety of high-impact biological challenges.

Responsibilities

• Develop new image analysis modules including a variety of computational approaches for the following tasks: segmentation of features in 2D/3D, analysis of signal intensity, spectral unmixing algorithms compatible with different types of fluorescence microscopes; deconvolution of intensities in sparsely to densely populated images.
• Develop intuitive visualization/plotting of analysis output, QC output and results.
• Develop QC tools both for internal development and for customers.
• Systematic and critical evaluation of automated analysis to ensure quality of analysis.
• Routinely interact with R&D team to strike optimal performance balance between the bioassay and image analysis.
• Provide routine support to R&D and service teams in the context of assay development, execution and troubleshooting according to internal and customer feedback.
• Collaborate and contribute to interdisciplinary research teams that include chemists and biologists.
• Provide software support for customers and create ad hocs for different imaging systems.
• Create high-quality, robust implementations of algorithms that will perform in the hands of both the R&D team and external customers.
• Support data processing and data visualization activities.
• Maintain plans and reach goals on time.
• Document and report experimental results.
• Assist in risk management.
• Keeping up to date with relevant scientific and technical developments within image analysis.

Skills & Requirements

We are looking for a candidate with demonstrated image analysis skills, a focused mindset, desire to have an impact in biomolecular analysis and meticulous attention to detail. It is preferred if the candidate has previously worked with image analysis of fluorescence (microscopy) images. The right person has a strategic, action driven mindset with flexibility in changing direction and methods within a fast-paced environment, as well as the capacity of managing multiple priorities and ability to efficiently communicate with all levels within the organization to find efficient ways to reach goals and milestones.

Minimum requirements:

• MSc or PhD degree in bioinformatics, computational biology, computer science, biomedical engineering, biotechnology, physics, or related fields.
• Experience with large-scale imaging data and formats.
• Support the development of strong customer/client relationships.
• Ability to quickly develop custom analysis methods and algorithms and apply them to large data sets.
• Expert level experience in relevant computational toolsets (e.g., programming languages such as Python, image analysis packages such as OpenCV and machine learning tools such as Pytorch, Keras and Tensorflow).
• Ability to Perform model training & evaluation for semantic segmentation, object detection, and instance segmentation tasks.
• Valid permission to work in Sweden.
• Excellent oral and written communication skills in English.

Preferred requirements:

• Minimum 2 years industry experience is an advantage.
• Experience with fluorescence microscopy is highly regarded.
• Knowledge of general-purpose machine learning skills (e.g., classification, fitting & regression, optimization methods) is highly regarded.
• Experience with image analysis in the context of spatial transcriptomics/proteomics (e.g., smFISH, in-situ sequencing, PLA etc.) is highly regarded.

Terms of employment

This is a full-time salary position available immediately, with a 6-months probational period that can lead to full-time employment. The position is based on site in Aplex Bio’s facility on KI campus.