recOrder: Open-source pipeline for computational imaging of physical and molecular architecture (SPIE-ABC 2021)

Lightning presentation for SPIE Advanced Biophotonics Conference 2021.

Abstract:

Correlative label-free and fluorescence imaging enables comprehensive and scalable mapping of the architectural order of biological systems to investigate a wide variety of questions in tissue pathology and live-cell dynamics.  Current imaging techniques require tight integration of complex optical systems and computational reconstruction methods that are often inaccessible to the end user.  We report an open-source computational imaging platform, recOrder, which enables the integration of quantitative label-free imaging with phase and polarization (QLIPP) with an existing fluorescence microscope via open-source acquisition and analysis software. recOrder enables a user to efficiently calibrate the light path, acquire 4D multi-modal volumes, reconstruct both label-free and fluorescence volumes, and readily visualize the data.  The recOrder platform leverages pycromanager and Micro-Manager for pythonic control of the components of the microscope and napari for pythonic visualization of and interaction with high-dimensional data.  recOrder enabled systematic measurements of changes in the architectural order of mouse brain tissue sections due to developmental mutations. We optimized the acquisition speed of the QLIPP to enable faster imaging of a 3D anisotropy and density, allowing the user to measure architectural changes of live cells. recOrder enabled automated imaging of the label-free and fluorescence volumes of endogenously tagged cell lines from OpenCell collection, with and without perturbations. These advances in modular and integrative computational imaging facilitate efficient integration of quantitative, label-free imaging into existing high throughput imaging pipelines to provide complimentary measurements of the architectural order of cells and tissues.