ArticleRadiation oncology (London, England)2015
The Focinator - a new open-source tool for high-throughput foci evaluation of DNA damage.
Article in Radiation oncology (London, England), 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 33 papers.
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Who cites it
33 citing papers in PubMed, 55 citations in OpenAlex.
- Tumor-Specific Antigen Delivery for T-cell Therapy via a pH-Sensitive Peptide Conjugate.Molecular cancer therapeutics · 2025Article
- Extracellular Vesicles from Plasma of Patients with Glioblastoma Promote Invasion of Glioblastoma Cells Even After Tumor Resection.Biomedicines · 2024Article
- Foci-Xpress: Automated and Fast Nuclear Foci Counting Tool.International journal of molecular sciences · 2023Article
- Rif1 restrains the rate of replication origin firing in Xenopus laevis.Communications biology · 2023Article
- Topical Capsaicin in Poly(lactic-co-glycolic)acid (PLGA) Nanoparticles Decreases Acute Itch and Heat Pain.International journal of molecular sciences · 2022Article
- A deep learning model (FociRad) for automated detection of γ-H2AX foci and radiation dose estimation.Scientific reports · 2022Article
- Metabolism of cancer cells commonly responds to irradiation by a transient early mitochondrial shutdown.iScience · 2021Article
- PLA2R1 promotes DNA damage and inhibits spontaneous tumor formation during aging.Cell death & disease · 2021Article
- Differential immunomodulatory effect of PARP inhibition in BRCA1 deficient and competent tumor cells.Biochemical pharmacology · 2021Article
- DeepFoci: Deep learning-based algorithm for fast automatic analysis of DNA double-strand break ionizing radiation-induced foci.Computational and structural biotechnology journal · 2021Article
- Review
- Caveolin-1 regulates the ASMase/ceramide-mediated radiation response of endothelial cells in the context of tumor-stroma interactions.Cell death & disease · 2020Article
- Article
- FocAn: automated 3D analysis of DNA repair foci in image stacks acquired by confocal fluorescence microscopy.BMC bioinformatics · 2020Article
- Topoisomerase IB poisons induce histone H2A phosphorylation as a response to DNA damage in Leishmania infantum.International journal for parasitology. Drugs and drug resistance · 2019Article
- Mitochondrial DNA Stress Signalling Protects the Nuclear Genome.Nature metabolism · 2019Article
- Article
- MODELLING γ-H2AX FOCI INDUCTION TO MIMIC LIMITATIONS IN THE SCORING TECHNIQUE.Radiation protection dosimetry · 2019Article
- The nuclear interactome of DYRK1A reveals a functional role in DNA damage repair.Scientific reports · 2019Article
- High-throughput Evaluation of Protein Migration and Localization after Laser Micro-Irradiation.Scientific reports · 2019Article
Corrections and comments
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Authors and funding
5 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundThe quantitative analysis of foci plays an important role in many cell biological methods such as counting of colonies or cells, organelles or vesicles, or the number of protein complexes. In radiation biology and molecular radiation oncology, DNA damage and DNA repair kinetics upon ionizing radiation (IR) are evaluated by counting protein clusters or accumulations of phosphorylated proteins recruited to DNA damage sites. Consistency in counting and interpretation of foci remains challenging. Many current software solutions describe instructions for time-consuming and error-prone manual analysis, provide incomplete algorithms for analysis or are expensive. Therefore, we aimed to develop a tool for costless, automated, quantitative and qualitative analysis of foci.
methodsFor this purpose we integrated a user-friendly interface into ImageJ and selected parameters to allow automated selection of regions of interest (ROIs) depending on their size and circularity. We added different export options and a batch analysis. The use of the Focinator was tested by analyzing γ-H2.AX foci in murine prostate adenocarcinoma cells (TRAMP-C1) at different time points after IR with 0.5 to 3 Gray (Gy). Additionally, measurements were performed by users with different backgrounds and experience.
resultsThe Focinator turned out to be an easily adjustable tool for automation of foci counting. It significantly reduced the analysis time of radiation-induced DNA-damage foci. Furthermore, different user groups were able to achieve a similar counting velocity. Importantly, there was no difference in nuclei detection between the Focinator and ImageJ alone.
conclusionsThe Focinator is a costless, user-friendly tool for fast high-throughput evaluation of DNA repair foci. The macro allows improved foci evaluation regarding accuracy, reproducibility and analysis speed compared to manual analysis. As innovative option, the macro offers a combination of multichannel evaluation including colocalization analysis and the possibility to run all analyses in a batch mode.
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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.