Capillary stall quantification from optical coherence tomography angiogram maximum intensity projections

Abstract

Optical coherence tomography (OCT) is applicable to the study of cerebral microvasculature in vivo. Optimised acquisition schemes enable the generation of three-dimensional OCT angiograms, i.e., volumetric images of red blood cell flux in capillary networks, currently at a repetition rate of up to 1/10 seconds. This makes testable a new class of hypotheses that strive to bridge the gap between microscopic phenomena occurring at the spatial scale of neurons, and less invasive but crude techniques to measure macroscopic blood flow dynamics. Here we present a method for quantifying the occurrence of transient capillary stalls in OCT angiograms, i.e., events during which blood flow through a capillary branch is temporarily occluded. By making the assumption that information on such events is present predominantly in the imaging plane, we implemented a pipeline that automatically segments a network of interconnected capillaries from the maximum intensity projections (MIP) of a series of 3D angiograms. We then developed tools enabling rapid manual assessment of the binary flow status (open/stalled) of hundreds of capillary segments based on the intensity profile of each segment across time. The entire pipeline is optimized to run on a standard laptop computer, requiring no high-performance, low-availability resources, despite very large data volumes. To further reduce the threshold of adoption, and ultimately to support the development of reproducible research methods in the young field, we provide the documented code for scrutiny and re-use under a permissive open-source license.

Disturbed microcirculation and hyperaemic response in a murine model of systemic inflammation

“…We developed a novel pipeline for semi-automatic detection of capillary stalls, which is fully documented in preprint form. 27 Links to code and validation datasets can be found on the project’s OSF homepage at https://osf.io/me6hf/ . Briefly, we first extracted a thin slab (400 × 400 × 20 voxels) from the angiogram, corresponding to the volume of tissue that is maximally in focus.…”

Evaluation of cerebral microcirculation in a mouse model of systemic inflammation

“…In the present study, we employed an open-source image processing analysis tool developed by S. Fruekilde. 8 , 10 To outline the methodology briefly, the frames were initially transformed into 3D angiograms. Subsequently, 3D angiogram slabs were extracted and flattened en face using a maximum intensity projection technique along the Z-dimension, resulting in the generation of 60 flattened images (one per frame).…”

“…Compared with traditional techniques utilized for studying of capillary stalling, including two-photon microscopy 36 and OCT, 8 , 10 it is noteworthy that the application of fluorescent optical imaging could represents a simpler approach in the investigation of capillary stalling. It offers a direct, expeditious, and comprehensive means of gaining insights into the mechanisms of micro cerebral circulation, and improving and specializing the simulations done here will potentially yield a validated biomarker that can help investigate this elusive phenomenon.…”

“…The requirement of injecting contrast agents for the visualization of vascular structures may also alter the phenomenon at hand. This led to the application of optical coherence tomography (OCT), 8 – 10 which can obtain volumetric angiograms at a high speed while preserving capillary-level resolution without exogenous contrast. It thus provides an efficient method for studying the mechanism of capillary stalling.…”