iCLOTS: open-source, artificial intelligence-enabled software for analyses of blood cells in microfluidic and microscopy-based assays

Abstract

While microscopy-based cellular assays, including microfluidics, have significantly advanced over the last several decades, there has not been concurrent development of widely-accessible techniques to analyze time-dependent microscopy data incorporating phenomena such as fluid flow and dynamic cell adhesion. As such, experimentalists typically rely on error-prone and time-consuming manual analysis, resulting in lost resolution and missed opportunities for innovative metrics. We present a user-adaptable toolkit packaged into the open-source, standalone Interactive Cellular assay Labeled Observation and Tracking Software (iCLOTS). We benchmark cell adhesion, single-cell tracking, velocity profile, and multiscale microfluidic-centric applications with blood samples, the prototypical biofluid specimen. Moreover, machine learning algorithms characterize previously imperceptible data groupings from numerical outputs. Free to download/use, iCLOTS addresses a need for a field stymied by a lack of analytical tools for innovative, physiologically-relevant assays of any design, democratizing use of well-validated algorithms for all end-user biomedical researchers who would benefit from advanced computational methods.

Total Synthesis of a PSGL-1 Glycopeptide Analogue for Targeted Inhibition of P-Selectin

“…Blood from children (ages 2 to 18 years) with SCD ( n = 10), already maintained on hydroxyurea, was recalcified and perfused for 25 min through the lab-on-chip system in the presence or absence of GSnP-6 (120 μM). Immediately following perfusion, devices were imaged, and occlusion was quantified using iClots, an open-source stand-alone software that uses predefined workflows based upon well-validated image processing and algorithms to measure the percentage of occluded microchannels . Treatment with GSnP-6 led to a marked reduction of vaso-occlusive events ( p < 0.009) (Figure C).…”

“…Immediately following perfusion, devices were imaged, and occlusion was quantified using iClots, an open-source stand-alone software that uses predefined workflows based upon well-validated image processing and algorithms to measure the percentage of occluded microchannels. 65 Treatment with GSnP-6 led to a marked reduction of vaso-occlusive events (p < 0.009) (Figure 1C). The degree to which thrombosis was attenuated in a given individual by GSnP-6 was unrelated to the measured percentage of hemoglobin S or the total concentration of hemoglobin (Supporting Figure 1).…”