Evidence map›Paper›PMID 40885286›Full record

ArticleSLAS discovery : advancing life sciences R & D2025

Alternate dyes for image-based profiling assays.

Suganya Sivagurunathan, Patrick Byrne, Alán F Muñoz, John Arevalo, Anne E Carpenter, Shantanu Singh, Maria Kost-Alimova, Beth A Cimini

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Article in SLAS discovery : advancing life sciences R & D, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 3 papers.

0numbers the graph read from it
0cells of the map it votes in
3citing 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

3 citing papers in PubMed.

  1. Article
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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

8 authors.

Suganya SivagurunathanImaging Platform, Broad Institute of MIT and Harvard, Cambridge, MA, USA.
Patrick ByrneThe Center for the Development of Therapeutics, Broad Institute of MIT and Harvard, Cambridge, MA, USA.
Alán F MuñozImaging Platform, Broad Institute of MIT and Harvard, Cambridge, MA, USA.
John ArevaloImaging Platform, Broad Institute of MIT and Harvard, Cambridge, MA, USA.
Anne E CarpenterImaging Platform, Broad Institute of MIT and Harvard, Cambridge, MA, USA.
Shantanu SinghImaging Platform, Broad Institute of MIT and Harvard, Cambridge, MA, USA.
Maria Kost-AlimovaThe Center for the Development of Therapeutics, Broad Institute of MIT and Harvard, Cambridge, MA, USA.
Beth A CiminiImaging Platform, Broad Institute of MIT and Harvard, Cambridge, MA, USA. Electronic address: bcimini@broadinstitute.org.

Funding

Extracting rich information from biological imagesR35GM122547 · NIGMS · BROAD INSTITUTE, INC. · PI Anne E. Carpenter · 2017 to 2026
$6.2M
Opera Phenix high-throughput microplate confocal imager for high-content screeningS10OD026839 · OD · BROAD INSTITUTE, INC. · PI WAGNER, BRIDGET K · 2019 to 2019
$1.0M
NIGMS NIH HHS R35 GM122547NIH HHS S10 OD026839
6 · The paper itself

Abstract

backgroundCell Painting, the leading image-based profiling assay, involves staining plated cells with six dyes that mark the different compartments in a cell. Such profiles can then be used to discover connections between samples (whether different cell lines, different genetic treatments, or different compound treatments) as well as to assess particular features impacted by each treatment. Researchers may wish to vary the standard dye panel to assess particular phenotypes, or image cells live while maintaining the ability to cluster profiles overall.

methodsIn this study, we evaluate the performance of dyes that can either replace or augment the traditional Cell Painting dyes or enable tracking live cell dynamics. We perturbed U2OS cells with 90 different compounds and subsequently stained them with either standard Cell Painting dyes (Revvity), or with MitoBrilliant (Tocris) replacing MitoTracker or Phenovue phalloidin 400LS (Revvity) replacing phalloidin. We also tested the live-cell compatible ChromaLive dye (Saguaro).

resultsAll dye sets effectively separated biological replicates of the same sample vs. negative controls (phenotypic activity), although separating from replicates of all other compounds (phenotypic distinctiveness) proved challenging for all dye sets. While individual dye substitutions within the standard Cell Painting panel had minimal impact on assay performance, the live cell dye exhibited distinct performance profiles across different compound classes compared to the standard panel, with later time points more distinct than earlier ones. DISCUSSION: Substituting MitoBrilliant or Phenovue phalloidin 400LS for standard mitochondrial or actin dyes minimally impacted Cell Painting assay performance. Phenovue phalloidin 400LS offers the advantage of isolating actin features from Golgi or plasma membrane while accommodating an additional 568 nm dye. Live cell imaging, enabled by ChromaLive dye, provides real-time assessment of compound-induced morphological changes. Combining this with the standard Cell Painting assay significantly expands the feature space for enhanced cellular profiling. Our findings provide data-driven options for researchers selecting dye sets for image-based profiling.

Indexed as

Coloring AgentsFluorescent DyesCell Line, TumorHumansStaining and LabelingColoring AgentsFluorescent DyesCell paintingChromaLiveHigh content screeningImage-based profilesLive cell paintingMitoBrilliantMorphological profilingPhenotypic screeningPhenovue phalloidin 400LS

Identifiers

PMID40885286
PMCPMC12794378

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Registered trials

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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.