ESC-Track: A computer workflow for 4-D segmentation, tracking, lineage tracing and dynamic context analysis of ESCs
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 develop...
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| Format: | Article |
| Language: | English |
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Taylor & Francis Group
2017-05-01
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| Series: | BioTechniques |
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| Online Access: | https://www.future-science.com/doi/10.2144/000114545 |
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| author | Laura Fernández-de-Manúel Covadonga Díaz-Díaz Daniel Jiménez-Carretero Miguel Torres María C. Montoya |
| author_facet | Laura Fernández-de-Manúel Covadonga Díaz-Díaz Daniel Jiménez-Carretero Miguel Torres María C. Montoya |
| author_sort | Laura Fernández-de-Manúel |
| collection | DOAJ |
| description | 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 evaluation of the genealogical and microenvironmental cues that maintain ESC fitness. |
| format | Article |
| id | doaj-art-7fe2ac33ff0d46ed8d45d7e3cf3d35a4 |
| institution | OA Journals |
| issn | 0736-6205 1940-9818 |
| language | English |
| publishDate | 2017-05-01 |
| publisher | Taylor & Francis Group |
| record_format | Article |
| series | BioTechniques |
| spelling | doaj-art-7fe2ac33ff0d46ed8d45d7e3cf3d35a42025-08-20T02:26:03ZengTaylor & Francis GroupBioTechniques0736-62051940-98182017-05-0162521522210.2144/000114545ESC-Track: A computer workflow for 4-D segmentation, tracking, lineage tracing and dynamic context analysis of ESCsLaura Fernández-de-Manúel0Covadonga Díaz-Díaz1Daniel Jiménez-Carretero2Miguel Torres3María C. Montoya41Cellomics Unit2Cardiovascular Developmental Program, Cell & Developmental Biology Area, Centro Nacional de Investigaciones Cardiovasculares CNIC, Madrid, Spain1Cellomics Unit2Cardiovascular Developmental Program, Cell & Developmental Biology Area, Centro Nacional de Investigaciones Cardiovasculares CNIC, Madrid, Spain1Cellomics UnitEmbryonic 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 evaluation of the genealogical and microenvironmental cues that maintain ESC fitness.https://www.future-science.com/doi/10.2144/000114545ESCimage processingsegmentationtrackinglineage |
| spellingShingle | Laura Fernández-de-Manúel Covadonga Díaz-Díaz Daniel Jiménez-Carretero Miguel Torres María C. Montoya ESC-Track: A computer workflow for 4-D segmentation, tracking, lineage tracing and dynamic context analysis of ESCs BioTechniques ESC image processing segmentation tracking lineage |
| title | ESC-Track: A computer workflow for 4-D segmentation, tracking, lineage tracing and dynamic context analysis of ESCs |
| title_full | ESC-Track: A computer workflow for 4-D segmentation, tracking, lineage tracing and dynamic context analysis of ESCs |
| title_fullStr | ESC-Track: A computer workflow for 4-D segmentation, tracking, lineage tracing and dynamic context analysis of ESCs |
| title_full_unstemmed | ESC-Track: A computer workflow for 4-D segmentation, tracking, lineage tracing and dynamic context analysis of ESCs |
| title_short | ESC-Track: A computer workflow for 4-D segmentation, tracking, lineage tracing and dynamic context analysis of ESCs |
| title_sort | esc track a computer workflow for 4 d segmentation tracking lineage tracing and dynamic context analysis of escs |
| topic | ESC image processing segmentation tracking lineage |
| url | https://www.future-science.com/doi/10.2144/000114545 |
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