Evidence map›Paper›PMID 41746805›Full record

ArticleSTAR protocols2026

Protocol for automated analysis of biological images using Python code.

Benjamin Sacks, Jiya Mody, Yiming Huang, Sunghoo Jung, Robert Kimelman, Elena Eubanks, Elyse Guadagno, Jose Cevallos, Ananya Guntur, Neeharika Rao Suvvari and 5 more

Abstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in STAR protocols, 2026. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 1 paper.

0numbers the graph read from it
0cells of the map it votes in
1citing 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

1 citing paper in PubMed.

  1. 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

15 authors.

Benjamin SacksDepartment of Neurology, Robert Wood Johnson Medical School, Institute for Neurological Therapeutics at Rutgers, Rutgers Biomedical and Health Sciences, Piscataway, NJ 08854, USA.
Jiya ModyDepartment of Neurology, Robert Wood Johnson Medical School, Institute for Neurological Therapeutics at Rutgers, Rutgers Biomedical and Health Sciences, Piscataway, NJ 08854, USA.
Yiming HuangDepartment of Neurology, Robert Wood Johnson Medical School, Institute for Neurological Therapeutics at Rutgers, Rutgers Biomedical and Health Sciences, Piscataway, NJ 08854, USA.
Sunghoo JungDepartment of Neurology, Robert Wood Johnson Medical School, Institute for Neurological Therapeutics at Rutgers, Rutgers Biomedical and Health Sciences, Piscataway, NJ 08854, USA.
Robert KimelmanDepartment of Neurology, Robert Wood Johnson Medical School, Institute for Neurological Therapeutics at Rutgers, Rutgers Biomedical and Health Sciences, Piscataway, NJ 08854, USA.
Elena EubanksDepartment of Neurology, Robert Wood Johnson Medical School, Institute for Neurological Therapeutics at Rutgers, Rutgers Biomedical and Health Sciences, Piscataway, NJ 08854, USA.
Elyse GuadagnoDepartment of Neurology, Robert Wood Johnson Medical School, Institute for Neurological Therapeutics at Rutgers, Rutgers Biomedical and Health Sciences, Piscataway, NJ 08854, USA.
Jose CevallosDepartment of Neurology, Robert Wood Johnson Medical School, Institute for Neurological Therapeutics at Rutgers, Rutgers Biomedical and Health Sciences, Piscataway, NJ 08854, USA.
Ananya GunturDepartment of Neurology, Robert Wood Johnson Medical School, Institute for Neurological Therapeutics at Rutgers, Rutgers Biomedical and Health Sciences, Piscataway, NJ 08854, USA.
Neeharika Rao SuvvariDepartment of Neurology, Robert Wood Johnson Medical School, Institute for Neurological Therapeutics at Rutgers, Rutgers Biomedical and Health Sciences, Piscataway, NJ 08854, USA.
Aryan DoshiDepartment of Neurology, Robert Wood Johnson Medical School, Institute for Neurological Therapeutics at Rutgers, Rutgers Biomedical and Health Sciences, Piscataway, NJ 08854, USA.
Nitya RavinutalaDepartment of Neurology, Robert Wood Johnson Medical School, Institute for Neurological Therapeutics at Rutgers, Rutgers Biomedical and Health Sciences, Piscataway, NJ 08854, USA.
Alejandro MoseraDepartment of Neurology, Robert Wood Johnson Medical School, Institute for Neurological Therapeutics at Rutgers, Rutgers Biomedical and Health Sciences, Piscataway, NJ 08854, USA.
Alessandro CrimiAGH University of Krakow, al. Adama Mickiewicza 30, 30-059 Kraków, Poland.
Eleanna KaraDepartment of Neurology, Robert Wood Johnson Medical School, Institute for Neurological Therapeutics at Rutgers, Rutgers Biomedical and Health Sciences, Piscataway, NJ 08854, USA. Electronic address: ek851@rwjms.rutgers.edu.

Funding

No grant is acknowledged in the PubMed record.

6 · The paper itself

Abstract

Image analysis in Python provides greater flexibility and an open-source alternative to commercially available software. In this protocol, we present steps for quantifying features in various common biological images in a manner that is tailored to scientists with little coding background. Using example experiments, we outline steps to read in a variety of image file types and prepare them for quantitative analysis. We then discuss approaches for segmenting images, extracting measurements from segmented images, and exporting data. For complete details on the use and execution of this protocol, please refer to Eubanks et al.

Indexed as

Image Processing, Computer-AssistedSoftwareAnimalsBioinformaticsCell BiologyComputer sciencesMicroscopy

Identifiers

PMID41746805
PMCPMC12955092

What OpenQuestion holds

Textmetadata
LicenceCC BY-NC-ND
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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.