2026-06-14T03:33:13Zhttps://repisalud.isciii.es/rest/oai/requestoai:repisalud.isciii.es:20.500.12105/98952024-09-27T07:59:04Zcom_20.500.12105_19604com_20.500.12105_2051col_20.500.12105_19605col_20.500.12105_19607
Repisalud
author
Fernandez-de-Manuel, Laura
author
Diaz-Diaz, Covadonga
author
Jimenez-Carretero, Daniel
author
Torres, Miguel
author
Montoya, Maria
funder
Ministerio de Economía y Competitividad (España)
funder
Unión Europea. Comisión Europea
funder
Comunidad de Madrid (España)
funder
Fundación ProCNIC
funder
Instituto de Salud Carlos III
2020-05-05T11:30:51Z
2020-05-05T11:30:51Z
2017-05
Biotechniques. 2017; 62(5):215-222
10.2144/000114545
1940-9818
1940-9818
BioTechniques
28528574
http://hdl.handle.net/20.500.12105/9895
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.
eng
ESC
Image processing
Lineage
Segmentation
Tracking
ESC-Track: A computer workflow for 4-D segmentation, tracking, lineage tracing and dynamic context analysis of ESCs
journal article
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
URL
https://repisalud.isciii.es/bitstreams/9b6f0b08-f38a-43b8-9d32-b267ddc7dd67/download
File
MD5
c0f177f58ceaf6bc737ab1f0632cc12d
662194
application/pdf
ESC‐TrackComputerWorkflow4‐D_2017.pdf
URL
https://repisalud.isciii.es/bitstreams/f4a62ef6-caa8-4358-a0dc-276ae52ac424/download
File
MD5
67c872644fbca5a86a63c45e954341e6
517547
application/pdf
Supplementary Materials and Methods.pdf
URL
https://repisalud.isciii.es/bitstreams/90999404-de3d-4d62-8084-158d9f1a7eac/download
File
MD5
da5103ba8207efb7f345644893d588c6
801146
application/octet-stream
Fernández-de-Manúel Supplementary Video S1.avi
URL
https://repisalud.isciii.es/bitstreams/3da8ab02-bb24-4fe9-842b-16a7adf4654e/download
File
MD5
e2efc55f09c2dbf2202837f7a53aa19c
183456
application/pdf
Fernández-de-Manúel Supplementary Video S1 Caption.pdf
URL
https://repisalud.isciii.es/bitstreams/40272bba-e36d-4466-8a62-9fa0ab407afc/download
File
MD5
e83b23dd10aab01c65ef1222dab0f006
371472
application/pdf
Fernández-de-Manúel Supplementary Table S1.pdf
URL
https://repisalud.isciii.es/bitstreams/8d6e4b1a-1866-4e9d-bfc2-6445b9f17500/download
File
MD5
94284f9bc2d24c228bc4257a6d3eeac6
14123847
image/tiff
Fig_1.tif
URL
https://repisalud.isciii.es/bitstreams/d499b39e-b1cb-4d45-996e-f32a5b607dd6/download
File
MD5
1374918eab8ae184bcf5a55668350509
4068990
image/tiff
Fig_4.tif
URL
https://repisalud.isciii.es/bitstreams/c095fa93-78a3-402a-b85f-d36db09227c8/download
File
MD5
97f11963e4e3dee174988040055ccb2e
580143
image/tiff
Fig_Sup.tif
URL
https://repisalud.isciii.es/bitstreams/f7780fd5-b1ee-48eb-ac12-40dea282deea/download
File
MD5
2a86955d9b2d5ee48b363a8b27ad81a1
8050266
image/tiff
Fig_2.tif
URL
https://repisalud.isciii.es/bitstreams/85595349-c41e-43be-9e1a-1eeeb110ef3c/download
File
MD5
65fe4ad99f5622dc768a7666d96699a3
13593730
image/tiff
Fig_3.tif
URL
https://repisalud.isciii.es/bitstreams/fc6a515c-fbef-49e6-84e1-317a10f57a6f/download
File
MD5
449d7b3250e2d7e9173efe7031770c3b
36020
text/plain
ESC‐TrackComputerWorkflow4‐D_2017.pdf.txt
URL
https://repisalud.isciii.es/bitstreams/ae2171e7-7273-487b-baf5-3e58ee6f7dbb/download
File
MD5
3b22615bca089ddbdebd25c42bad83b7
9312
text/plain
Supplementary Materials and Methods.pdf.txt
URL
https://repisalud.isciii.es/bitstreams/44676f03-bc82-4d67-8ae1-365e7d9edabe/download
File
MD5
8d70563d659704a93858889ec13c6b0c
838
text/plain
Fernández-de-Manúel Supplementary Video S1 Caption.pdf.txt
URL
https://repisalud.isciii.es/bitstreams/a1ed2464-7892-4ef3-bcc3-c5a8899d10c8/download
File
MD5
bc1fc9634e6f399ebe34a140f151f2dc
6643
text/plain
Fernández-de-Manúel Supplementary Table S1.pdf.txt