At the Rosalind Franklin Institute (Franklin), a specialized team of computer scientists is dedicated to developing software for interacting with large three-dimensional (3D) microscopic biology data sets.
Presently, state-of-art microscopy aims to collect a high-quality microscopic 3D picture of biological samples inside of cells. In one workflowto do this, the cells are cryogenically preserved, imaged using fluorescent light microscopy to find areas of interest, milled to show just those areas of interest and then data is collected. This raw data contains nanometer scale information of cellular compartments and their components (proteins, DNA, RNA, etc). The raw data is next computationally reconstructed into a 3D volume of data and regions within the data are annotated or segmented so that they can be analysed and the biological question answered.
It is very challenging to collect, process, and analyse these large datasets, especially when the analysis workflow includes correlative imaging and segmentation steps. The figure below illustrates the complexity of the data processing pipeline commonly involved in an experiment using cryogenic plasma FIB/SEM to create lamellae followed by cryogenic electron tomography to collect high resolution 3D volumes and then process them into a biologically relevant outcome.
The goal is to look at the analysis pipeline as a whole – volumetric imaging (e.g. scanning or transmission electron microscopy) and associated correlative imaging techniques (e.g. light or X-ray microscopy) data collection, reconstruction, segmentation, model building and analysis – and to make significant improvements to the automation, speed and accuracy of the pipeline. In the Artificial Intelligence and Informatics group (AI&I) at the Franklin we are automating these workflow steps to solve computationally difficult and time-intensive problems by developing cross platform open-source software tools. We also try to integrate with commonly used data analysis and visualisation software such as ImageJ and napari, and EM specialised software such as IMOD.
Current Projects
Image Assessment and Artefact Removal
Human In The Loop Processing
Automated Segmentation
Building Community