ArticleBiological imaging2022
Cell-TypeAnalyzer: A flexible Fiji/ImageJ plugin to classify cells according to user-defined criteria.
Article in Biological imaging, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 1 paper.
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Who cites it
1 citing paper in PubMed.
- ModelistsGCN: a multimodal graph convolutional network framework for single-cell spatial transcriptomic cell typing.Briefings in bioinformatics · 2026Article
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4 authors.
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Abstract
Fluorescence microscopy techniques have experienced a substantial increase in the visualization and analysis of many biological processes in life science. We describe a semiautomated and versatile tool called Cell-TypeAnalyzer to avoid the time-consuming and biased manual classification of cells according to cell types. It consists of an open-source plugin for Fiji or ImageJ to detect and classify cells in 2D images. Our workflow consists of (a) image preprocessing actions, data spatial calibration, and region of interest for analysis; (b) segmentation to isolate cells from background (optionally including user-defined preprocessing steps helping the identification of cells); (c) extraction of features from each cell; (d) filters to select relevant cells; (e) definition of specific criteria to be included in the different cell types; (f) cell classification; and (g) flexible analysis of the results. Our software provides a modular and flexible strategy to perform cell classification through a wizard-like graphical user interface in which the user is intuitively guided through each step of the analysis. This procedure may be applied in batch mode to multiple microscopy files. Once the analysis is set up, it can be automatically and efficiently performed on many images. The plugin does not require any programming skill and can analyze cells in many different acquisition setups.
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