ArticleJournal of cell science2022
GIANI - open-source software for automated analysis of 3D microscopy images.
Article in Journal of cell science, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 9 papers.
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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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Who cites it
9 citing papers in PubMed, 14 citations in OpenAlex.
- Epigenetic Compound Library Screen Identifies Ibrutinib as an Inhibitor of Ovarian Clear Cell Carcinoma Viability.Cancer medicine · 2026Article
- Article
- Nuclear instance segmentation and tracking for preimplantation mouse embryos.Development (Cambridge, England) · 2024Article
- VISION - an open-source software for automated multi-dimensional image analysis of cellular biophysics.Journal of cell science · 2024Article
- High-throughput image processing software for the study of nuclear architecture and gene expression.Scientific reports · 2024Article
- Defining the boundaries: challenges and advances in identifying cells in microscopy images.Current opinion in biotechnology · 2024Review
- 3D reconstruction of skin and spatial mapping of immune cell density, vascular distance and effects of sun exposure and aging.Communications biology · 2023Article
- Imaging developmental cell cycles.Biophysical journal · 2021Review
- HIV-1 requires capsid remodelling at the nuclear pore for nuclear entry and integration.PLoS pathogens · 2021Article
Corrections and comments
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Authors and funding
5 authors at 2 institutions in 2 countries.
Funding
Abstract
The study of cellular and developmental processes in physiologically relevant three-dimensional (3D) systems facilitates an understanding of mechanisms underlying cell fate, disease and injury. While cutting-edge microscopy technologies permit the routine acquisition of 3D datasets, there is currently a limited number of open-source software packages to analyse such images. Here, we describe General Image Analysis of Nuclei-based Images (GIANI; https://djpbarry.github.io/Giani), new software for the analysis of 3D images. The design primarily facilitates segmentation of nuclei and cells, followed by quantification of morphology and protein expression. GIANI enables routine and reproducible batch-processing of large numbers of images, and comes with scripting and command line tools. We demonstrate the utility of GIANI by quantifying cell morphology and protein expression in confocal images of mouse early embryos and by segmenting nuclei from light-sheet microscopy images of the flour beetle embryo. We also validate the performance of the software using simulated data. More generally, we anticipate that GIANI will be a useful tool for researchers in a variety of biomedical fields.
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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.