Evidence map›Paper›PMID 27286574›Full record

ArticleStem cell research2016

Large-scale time-lapse microscopy of Oct4 expression in human embryonic stem cell colonies.

Kiran Bhadriraju, Michael Halter, Julien Amelot, Peter Bajcsy, Joe Chalfoun, Antoine Vandecreme, Barbara S Mallon, Kye-Yoon Park, Subhash Sista, John T Elliott and 1 more

Abstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in Stem cell research, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 9 papers.

0numbers the graph read from it
0cells of the map it votes in
9citing papers in PubMed
–field-weighted citation impact
1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.

2 · The registry

The trial behind it

Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.

Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.

3 · Its place in the literature

Who cites it

9 citing papers in PubMed.

  1. Article
  2. Seabird Tissue Archival and Monitoring Project (STAMP) Data from 1999-2010.Journal of research of the National Institute of Standards and Technology · 2021
    Article
  3. Exact Tile-Based Segmentation Inference for Images Larger than GPU Memory.Journal of research of the National Institute of Standards and Technology · 2021
    Article
  4. Probing pluripotency gene regulatory networks with quantitative live cell imaging.Computational and structural biotechnology journal · 2020
    Review
  5. Article
  6. Review
  7. Article
  8. Article
  9. Article
4 · The record

Corrections and comments

PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.

5 · Who and what money

Authors and funding

11 authors.

Kiran BhadrirajuDepartment of Bioengineering, University of Maryland, College Park, MD 20742, USA.
Michael HalterBiosystems and Biomaterials Division, Materials Measurement Laboratory, National Institute of Standards and Technology, Gaithersburg, MD 20899, USA.
Julien AmelotSoftware Systems Division, Information Technology Laboratory, National Institute of Standards and Technology, Gaithersburg, MD 20899, USA.
Peter BajcsySoftware Systems Division, Information Technology Laboratory, National Institute of Standards and Technology, Gaithersburg, MD 20899, USA.
Joe ChalfounSoftware Systems Division, Information Technology Laboratory, National Institute of Standards and Technology, Gaithersburg, MD 20899, USA.
Antoine VandecremeSoftware Systems Division, Information Technology Laboratory, National Institute of Standards and Technology, Gaithersburg, MD 20899, USA.
Barbara S MallonThe NIH Stem Cell Unit, Division of Intramural Research, National Institute of Neurological Disorders and Stroke, NIH, U.S. Department of Health and Human Services, Bethesda, MD, USA.
Kye-Yoon ParkThe NIH Stem Cell Unit, Division of Intramural Research, National Institute of Neurological Disorders and Stroke, NIH, U.S. Department of Health and Human Services, Bethesda, MD, USA.
Subhash SistaBiosystems and Biomaterials Division, Materials Measurement Laboratory, National Institute of Standards and Technology, Gaithersburg, MD 20899, USA.
John T ElliottBiosystems and Biomaterials Division, Materials Measurement Laboratory, National Institute of Standards and Technology, Gaithersburg, MD 20899, USA.
Anne L PlantBiosystems and Biomaterials Division, Materials Measurement Laboratory, National Institute of Standards and Technology, Gaithersburg, MD 20899, USA.

Funding

Human pluripotent stem cellsZICNS003008 · NINDS · NATIONAL INSTITUTE OF NEUROLOGICAL DISORDERS AND STROKE · PI ROBEY, PAMELA · 2009 to 2025
$21.2M
Intramural NIH HHS Z99 NS999999
6 · The paper itself

Abstract

Identification and quantification of the characteristics of stem cell preparations is critical for understanding stem cell biology and for the development and manufacturing of stem cell based therapies. We have developed image analysis and visualization software that allows effective use of time-lapse microscopy to provide spatial and dynamic information from large numbers of human embryonic stem cell colonies. To achieve statistically relevant sampling, we examined >680 colonies from 3 different preparations of cells over 5days each, generating a total experimental dataset of 0.9 terabyte (TB). The 0.5 Giga-pixel images at each time point were represented by multi-resolution pyramids and visualized using the Deep Zoom Javascript library extended to support viewing Giga-pixel images over time and extracting data on individual colonies. We present a methodology that enables quantification of variations in nominally-identical preparations and between colonies, correlation of colony characteristics with Oct4 expression, and identification of rare events.

Indexed as

Image Processing, Computer-AssistedMicroscopy, FluorescenceTime-Lapse ImagingCell LineHuman Embryonic Stem CellsHumansOctamer Transcription Factor-3SoftwareOctamer Transcription Factor-3POU5F1 protein, humanCell therapyFluorescence microscopyLive cell imagingPluripotencyStem cells

Identifiers

PMID27286574
PMCPMC5012928

What OpenQuestion holds

Textmetadata
LicenceCC BY-NC-ND
Read underepoch 390

Registered trials

None linked

Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.