Search research articles

ABOUT JoVE

Overview Leadership Blog JoVE Help Center

AUTHORS

Publishing Process Editorial Board Scope & Policies Peer Review FAQ Submit

LIBRARIANS

Testimonials Subscriptions Access Resources Library Advisory Board FAQ

RESEARCH

JoVE Journal Methods Collections JoVE Encyclopedia of Experiments Archive

EDUCATION

JoVE Core JoVE Business JoVE Science Education JoVE Lab Manual Faculty Resource Center Faculty Site

Terms & Conditions of Use

Related Concept Videos

You might also read

Related Articles

Articles linked to this work by shared authors, journal, and citation graph.

Sort by

Same author

Stress Granule Sequestration of CCR4-NOT Promotes Poly(A) Lengthening of Stress-Survival Transcripts.

bioRxiv : the preprint server for biology·2026

Same author

High-content screening of organoids reveals the mechanisms of human pancreas acinar specification.

Cell stem cell·2026

Same author

Inhibition of TGF-beta signaling protects from alpha-synuclein induced toxicity.

Cell death discovery·2025

Same author

Small-molecule dissolution of stress granules by redox modulation benefits ALS models.

Nature chemical biology·2025

Same author

Human organoids with an autologous tissue-resident immune compartment.

Nature·2024

Same author

Modeling early pathophysiological phenotypes of diabetic retinopathy in a human inner blood-retinal barrier-on-a-chip.

Nature communications·2024

Same journal

Mapping the 3D Chromosome Organization of a Biosynthetic Gene Cluster by Capture Hi-C (CHi-C).

Methods in molecular biology (Clifton, N.J.)·2026

Same journal

Mapping the 3D Chromosome Organization of Streptomyces by Hi-C.

Methods in molecular biology (Clifton, N.J.)·2026

Same journal

CUT&Tag Epigenomic Profiling of Biosynthetic Gene Clusters in Arabidopsis thaliana.

Methods in molecular biology (Clifton, N.J.)·2026

Same journal

Rhizobium rhizogenes-Mediated Hairy Root Transformation Protocol for Lotus japonicus and Other Legumes.

Methods in molecular biology (Clifton, N.J.)·2026

Same journal

Characterization of Bioactive Saponins from Sea Cucumbers.

Methods in molecular biology (Clifton, N.J.)·2026

Same journal

Methods for Functional Validation of Terpenoid Metabolic Clusters in Nicotiana benthamiana and Aspergillus oryzae.

Methods in molecular biology (Clifton, N.J.)·2026

See all related articles

Search research articles

Related Experiment Video

Updated: May 13, 2026

Workflow for High-content, Individual Cell Quantification of Fluorescent Markers from Universal Microscope Data, Supported by Open Source Software

Workflow for High-content, Individual Cell Quantification of Fluorescent Markers from Universal Microscope Data, Supported by Open Source Software

Published on: December 16, 2014

CellProfiler and KNIME: open source tools for high content screening.

Martin Stöter¹, Antje Niederlein, Rico Barsacchi

¹Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany.

Methods in Molecular Biology (Clifton, N.J.)

|February 26, 2013

Summary

This summary is machine-generated.

High content screening (HCS) is becoming essential in academic research for drug discovery. Open-source software like CellProfiler and KNIME offer flexible and cost-effective solutions for analyzing large datasets, overcoming key limitations.

More Related Videos

High Content Screening in Neurodegenerative Diseases

High Content Screening in Neurodegenerative Diseases

Published on: January 6, 2012

Label-Free Immunoprecipitation Mass Spectrometry Workflow for Large-scale Nuclear Interactome Profiling

Label-Free Immunoprecipitation Mass Spectrometry Workflow for Large-scale Nuclear Interactome Profiling

Published on: November 17, 2019

Related Experiment Videos

Last Updated: May 13, 2026

Workflow for High-content, Individual Cell Quantification of Fluorescent Markers from Universal Microscope Data, Supported by Open Source Software

Workflow for High-content, Individual Cell Quantification of Fluorescent Markers from Universal Microscope Data, Supported by Open Source Software

Published on: December 16, 2014

High Content Screening in Neurodegenerative Diseases

High Content Screening in Neurodegenerative Diseases

Published on: January 6, 2012

Label-Free Immunoprecipitation Mass Spectrometry Workflow for Large-scale Nuclear Interactome Profiling

Label-Free Immunoprecipitation Mass Spectrometry Workflow for Large-scale Nuclear Interactome Profiling

Published on: November 17, 2019

Area of Science:

Biotechnology
Bioinformatics
Drug Discovery

Background:

High content screening (HCS) is a vital technology in pharmaceutical research for drug discovery and development.
HCS adoption is growing in academia, presenting opportunities for broader application.
Academic research faces unique challenges, including diverse assays and cost constraints, hindering HCS implementation.

Purpose of the Study:

To address the limitations of flexibility and cost in implementing High Content Screening (HCS) within academic research settings.
To introduce and evaluate open-source software solutions for HCS data analysis in academia.
To demonstrate how open-source tools can enhance the adaptability and affordability of HCS for diverse academic applications.

Main Methods:

Utilized CellProfiler, an open-source software, for high-content image analysis.
Employed KNIME, an open-source platform, for subsequent data analysis and data mining.
Evaluated the flexibility and cost-effectiveness of these open-source tools for academic HCS workflows.

Main Results:

CellProfiler provides robust image analysis capabilities suitable for varied academic assays.
KNIME offers a flexible and powerful environment for analyzing large HCS datasets and performing data mining.
The combined use of CellProfiler and KNIME significantly reduces software costs associated with HCS data analysis.
These open-source solutions enhance the adaptability of HCS setups for diverse academic research needs.

Conclusions:

Open-source software, specifically CellProfiler and KNIME, effectively addresses the cost and flexibility barriers for HCS in academia.
These tools empower academic researchers to leverage HCS for drug discovery and development with reduced financial and technical constraints.
The adoption of open-source solutions can accelerate the integration and expansion of HCS technology in academic research environments.