ESC-Track: A computer workflow for 4-D segmentation, tracking, lineage tracing and dynamic context analysis of ESCs

BioTechniques
Laura Fernández-de-ManúelMaría C Montoya

Abstract

Embryonic stem cells (ESCs) can be established as permanent cell lines, and their potential to differentiate into adult tissues has led to widespread use for studying the mechanisms and dynamics of stem cell differentiation and exploring strategies for tissue repair. Imaging live ESCs during development is now feasible due to advances in optical imaging and engineering of genetically encoded fluorescent reporters; however, a major limitation is the low spatio-temporal resolution of long-term 3-D imaging required for generational and neighboring reconstructions. Here, we present the ESC-Track (ESC-T) workflow, which includes an automated cell and nuclear segmentation and tracking tool for 4-D (3-D + time) confocal image data sets as well as a manual editing tool for visual inspection and error correction. ESC-T automatically identifies cell divisions and membrane contacts for lineage tree and neighborhood reconstruction and computes quantitative features from individual cell entities, enabling analysis of fluorescence signal dynamics and tracking of cell morphology and motion. We use ESC-T to examine Myc intensity fluctuations in the context of mouse ESC (mESC) lineage and neighborhood relationships. ESC-T is a powerful tool for...Continue Reading

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Citations

Feb 2, 2019·PloS One·Tristan A SharpAndrea J Liu
Apr 9, 2019·ELife·Sergio MencheroMiguel Manzanares

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Methods Mentioned

BETA
Profiler
feature extraction
confocal microscopy

Software Mentioned

TGMM
ESC
Track
ACME
EDGE
tTt
RACE
ImageJ
TrackMate
Icy

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