Dataset Information

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.

SUBMITTER: Fay ME

PROVIDER: S-EPMC10439163 | biostudies-literature | 2023 Aug

REPOSITORIES: biostudies-literature

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

Fay Meredith E ME Oshinowo Oluwamayokun O Iffrig Elizabeth E Fibben Kirby S KS Caruso Christina C Hansen Scott S Musick Jamie O JO Valdez José M JM Azer Sally S SS Mannino Robert G RG Choi Hyoann H Zhang Dan Y DY Williams Evelyn K EK Evans Erica N EN Kanne Celeste K CK Kemp Melissa L ML Sheehan Vivien A VA Carden Marcus A MA Bennett Carolyn M CM Wood David K DK Lam Wilbur A WA

Nature communications 20230818 1

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-ad ...[more]

PMID: 37596311

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Project description:MotivationAdvances in microscopy technology have led to the creation of high-throughput microscopes that are capable of generating several hundred gigabytes of images in a few days. Analyzing such wealth of data manually is nearly impossible and requires an automated approach. There are at present a number of open-source and commercial software packages that allow the user to apply algorithms of different degrees of sophistication to the images and extract desired metrics. However, the types of metrics that can be extracted are severely limited by the specific image processing algorithms that the application implements, and by the expertise of the user. In most commercial software, code unavailability prevents implementation by the end user of newly developed algorithms better suited for a particular type of imaging assay. While it is possible to implement new algorithms in open-source software, rewiring an image processing application requires a high degree of expertise. To obviate these limitations, we have developed an open-source high-throughput application that allows implementation of different biological assays such as cell tracking or ancestry recording, through the use of small, relatively simple image processing modules connected into sophisticated imaging pipelines. By connecting modules, non-expert users can apply the particular combination of well-established and novel algorithms developed by us and others that are best suited for each individual assay type. In addition, our data exploration and visualization modules make it easy to discover or select specific cell phenotypes from a heterogeneous population.AvailabilityCellAnimation is distributed under the Creative Commons Attribution-NonCommercial 3.0 Unported license (http://creativecommons.org/licenses/by-nc/3.0/). CellAnimationsource code and documentation may be downloaded from www.vanderbilt.edu/viibre/software/documents/CellAnimation.zip. Sample data are available at www.vanderbilt.edu/viibre/software/documents/movies.zip.Contactwalter.georgescu@vanderbilt.eduSupplementary informationSupplementary data available at Bioinformatics online.

Project description:BackgroundThe use of patient health and treatment information captured in structured and unstructured formats in computerized electronic health record (EHR) repositories could potentially augment the detection of safety signals for drug products regulated by the US Food and Drug Administration (FDA). Natural language processing and other artificial intelligence (AI) techniques provide novel methodologies that could be leveraged to extract clinically useful information from EHR resources.ObjectiveOur aim is to develop a novel AI-enabled software prototype to identify adverse drug event (ADE) safety signals from free-text discharge summaries in EHRs to enhance opioid drug safety and research activities at the FDA.MethodsWe developed a prototype for web-based software that leverages keyword and trigger-phrase searching with rule-based algorithms and deep learning to extract candidate ADEs for specific opioid drugs from discharge summaries in the Medical Information Mart for Intensive Care III (MIMIC III) database. The prototype uses MedSpacy components to identify relevant sections of discharge summaries and a pretrained natural language processing (NLP) model, Spark NLP for Healthcare, for named entity recognition. Fifteen FDA staff members provided feedback on the prototype's features and functionalities.ResultsUsing the prototype, we were able to identify known, labeled, opioid-related adverse drug reactions from text in EHRs. The AI-enabled model achieved accuracy, recall, precision, and F1-scores of 0.66, 0.69, 0.64, and 0.67, respectively. FDA participants assessed the prototype as highly desirable in user satisfaction, visualizations, and in the potential to support drug safety signal detection for opioid drugs from EHR data while saving time and manual effort. Actionable design recommendations included (1) enlarging the tabs and visualizations; (2) enabling more flexibility and customizations to fit end users' individual needs; (3) providing additional instructional resources; (4) adding multiple graph export functionality; and (5) adding project summaries.ConclusionsThe novel prototype uses innovative AI-based techniques to automate searching for, extracting, and analyzing clinically useful information captured in unstructured text in EHRs. It increases efficiency in harnessing real-world data for opioid drug safety and increases the usability of the data to support regulatory review while decreasing the manual research burden.

Dataset Information

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

Publications

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

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