ArticleCurrent protocols2021
ImageJ and CellProfiler: Complements in Open-Source Bioimage Analysis.
Article in Current protocols, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 20 papers.
What it found
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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.
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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.
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Who cites it
20 citing papers in PubMed.
- Data Management Workflow for FAIR Sharing of Bioimaging Datasets in Plasma Medicine.Scientific data · 2026Article
- Characterization of selected LDLR substitutions in patients with familial hypercholesterolemia.Atherosclerosis plus · 2025Article
- Deep Learning-Based Imaging Analysis Reveals Radiation-Induced Bystander Effects on Cancer Cell Migration and the Modulation by Cisplatin.International journal of molecular sciences · 2025Article
- Cellpose as a reliable method for single-cell segmentation of autofluorescence microscopy images.Scientific reports · 2025Article
- Article
- Spatial regulation of substrate adhesion directs fibroblast morphotype and phenotype.PNAS nexus · 2024Article
- Cellpose as a reliable method for single-cell segmentation of autofluorescence microscopy images.bioRxiv : the preprint server for biology · 2024Article
- SciJava Ops: an improved algorithms framework for Fiji and beyond.Frontiers in bioinformatics · 2024Article
- Hypomyelination, hypodontia and craniofacial abnormalities in a Polr3b mouse model of leukodystrophy.Brain : a journal of neurology · 2023Article
- Optimizing the Cell Painting assay for image-based profiling.Nature protocols · 2023Review
- An Automated Cell Detection Method for TH-positive Dopaminergic Neurons in a Mouse Model of Parkinson's Disease Using Convolutional Neural Networks.Experimental neurobiology · 2023Article
- A symbiotic physical niche in Drosophila melanogaster regulates stable association of a multi-species gut microbiota.Nature communications · 2023Article
- Autophagy profiling in single cells with open source CellProfiler-based image analysis.Autophagy · 2023Article
- A review of open-source image analysis tools for mammalian cell culture: algorithms, features and implementations.PeerJ. Computer science · 2023Article
- The Role of Pathology-Based Methods in Qualitative and Quantitative Approaches to Cancer Immunotherapy.Cancers · 2022Review
- An image analysis protocol using CellProfiler for automated quantification of post-ischemic cardiac parameters.STAR protocols · 2022Article
- Using the Power of Junctional Adhesion Molecules Combined with the Target of CAR-T to Inhibit Cancer Proliferation, Metastasis and Eradicate Tumors.Biomedicines · 2022Article
- A high-throughput assay for directly monitoring nucleolar rRNA biogenesis.Open biology · 2022Article
- Cell-TypeAnalyzer: A flexible Fiji/ImageJ plugin to classify cells according to user-defined criteria.Biological imaging · 2022Article
- Bioimage analysis workflows: community resources to navigate through a complex ecosystem.F1000Research · 2021Article
Corrections and comments
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Authors and funding
6 authors.
Funding
Abstract
ImageJ and CellProfiler have long been leading open-source platforms in the field of bioimage analysis. ImageJ's traditional strength is in single-image processing and investigation, while CellProfiler is designed for building large-scale, modular analysis pipelines. Although many image analysis problems can be well solved with one or the other, using these two platforms together in a single workflow can be powerful. Here, we share two pipelines demonstrating mechanisms for productively and conveniently integrating ImageJ and CellProfiler for (1) studying cell morphology and migration via tracking, and (2) advanced stitching techniques for handling large, tiled image sets to improve segmentation. No single platform can provide all the key and most efficient functionality needed for all studies. While both programs can be and are often used separately, these pipelines demonstrate the benefits of using them together for image analysis workflows. ImageJ and CellProfiler are both committed to interoperability between their platforms, with ongoing development to improve how both are leveraged from the other. © 2021 Wiley Periodicals LLC. Basic Protocol 1: Studying cell morphology and cell migration in time-lapse datasets using TrackMate (Fiji) and CellProfiler Basic Protocol 2: Creating whole plate montages to easily assess adaptability of segmentation parameters.
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Registered trials
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.