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[CellProfiler](https://cellprofiler.org/) {cite}`Stirling2021-sg` is a software designed for biologists by biologists; it creates a bridge between image analysis and scientist with no need of computational expertise. It was designed with the idea of an image analysis pipeline in mind: it allows you to take a series of interoperable modules to design your own custom analysis pipeline that can be applied to one or thousands of images, making it suitable for high throughput image analysis.
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[QuPath](https://qupath.github.io/) {cite}`Bankhead2017-kz` offers a wide set of image analysis tools that can be applied to whole slide images. For that reason it is widely utilized with pathology images, but it can be used with other images as well. QuPath also contains pixel classification tools and can integrate with ImageJ (e.g., for sending {term}`ROIs` between the programs, or for accessing ImageJ plugins).
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[MIB](http://mib.helsinki.fi/index.html) {cite}`Belevich2016-vi` is a user-friendly software for image analysis of multidimensional datasets for both light and electron microscopy. It allows you to use the whole acquired data for its analysis and extraction of morphological features.
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[napari](https://napari.org/) {cite}`Sofroniew2022-nd` is being developed as a multi-dimensional image viewer that can be expanded via a variety of plugins to perform basic and complex image analysis tasks.
[CellProfiler](https://cellprofiler.org/) was designed with the idea of an image analysis pipeline in mind; it allows you to take a series of interoperable modules to design your own custom analysis pipeline that can be applied to one or thousands of images, making it suitable for high throughput image analysis.
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[QuPath](https://qupath.github.io/) offers a wide set of image analysis tools that can be applied to whole slide images like pathology images, but it can be used with other images as well. QuPath also contains pixel classification tools and can integrate with ImageJ.
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[MIB](http://mib.helsinki.fi/index.html) is a user-friendly software for image analysis of multidimensional datasets for both light and electron microscopy. It allows you to use the whole acquired data for its analysis and extraction of morphological features.
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[napari](https://napari.org/) is being developed as a multi-dimensional image viewer that can be expanded via a variety of plugins to perform basic and complex image analysis tasks.
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[ilastik](https://www.ilastik.org/) is a tool for interactive image classification, {term}`segmentation` and analysis. It leverages machine-learning algorithms to perform pixel and object-level classification. Using it requires no experience in {term}`image processing`.
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[Piximi](https://www.piximi.app/) is an application for annotation and classification that runs entirely from your browser and requires no installation and minimal setup.
[ilastik](https://www.ilastik.org/) {cite}`Berg2019-no` is a tool for interactive image classification, {term}`segmentation` and analysis. It leverages machine-learning algorithms to perform pixel and object-level classification. Using it requires no experience in {term}`image processing`.
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[Piximi](https://www.piximi.app/) is an application for annotation and classification that runs entirely from your browser and requires no installation and minimal setup.
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