Publication

A Single-organoid Workflow for quantitative Imaging classiFication and Tracking (SWIFT)

2026

Abstract

SWIFT (Single-organoid Workflow for quantitative Imaging classiFication and Tracking) is a fast and modular pipeline for quantitative, time-resolved organoid analysis from brightfield images. Requiring only minimal training annotations, SWIFT combines YOLOv8, SAM, and application-specific object classification to deliver accurate single-organoid segmentation, phenotyping, and tracking. The workflow is robust across organoid types and microscope systems. Applied to intestinal organoids, SWIFT uncovers dynamic Wnt-dependent morphological transitions, enabling scalable, high-throughput studies of epithelial plasticity.

Official source

https://infoscience.epfl.ch/entities/publication/7180ff15-5cdd-401f-ae3c-2dbf281a1b9b

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2026

Abstract

Official source

https://infoscience.epfl.ch/entities/publication/7180ff15-5cdd-401f-ae3c-2dbf281a1b9b

About this result

Related concepts (19)

Workflow

A workflow consists of an orchestrated and repeatable pattern of activity, enabled by the systematic organization of resources into processes that transform materials, provide services, or process information. It can be depicted as a sequence of operations, the work of a person or group, the work of an organization of staff, or one or more simple or complex mechanisms. From a more abstract or higher-level perspective, workflow may be considered a view or representation of real work.

Workflow engine

A workflow engine is a software application that manages business processes. It is a key component in workflow technology and typically makes use of a database server. A workflow engine manages and monitors the state of activities in a workflow, such as the processing and approval of a loan application form, and determines which new activity to transition to according to defined processes (workflows). The actions may be anything from saving an application form in a document management system to sending a reminder e-mail to users or escalating overdue items to management.

Scientific workflow system

A scientific workflow system is a specialized form of a workflow management system designed specifically to compose and execute a series of computational or data manipulation steps, or workflow, in a scientific application. Distributed scientists can collaborate on conducting large scale scientific experiments and knowledge discovery applications using distributed systems of computing resources, data sets, and devices. Scientific workflow systems play an important role in enabling this vision.

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A Single-organoid Workflow for quantitative Imaging classiFication and Tracking (SWIFT)

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