Synonyms
Bioimage analysis

Napari image viewer

Description

napari is a fast, interactive, multi-dimensional image viewer for Python. It’s designed for browsing, annotating, and analyzing large multi-dimensional images. It’s built on top of Qt (for the GUI), vispy (for performant GPU-based rendering), and the scientific Python stack (e.g. numpyscipy). It includes critical viewer features out-of-the-box, such as support for large multi-dimensional data, and layering and annotation. By integrating closely with the Python ecosystem, napari can be easily coupled to leading machine learning and image analysis tools (e.g. scikit-imagescikit-learnTensorFlowPyTorch), enabling more user-friendly automated analysis.

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Icy Spot Tracking

Description

Up to version 2 it was known as the ‘Probabilistic particle tracker’ plugin.

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Icy Label Extractor

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Adaptive Pixel Representation

Description

A content-adaptive representation of fluorescence microscopy images called Adaptive Particle Representation (APR), which replaces the regular grid of pixels with particles positioned according to image content. This overcomes storage bottlenecks, as data compression does, but additionally overcomes memory and processing bottlenecks, since the APR can directly be used in processing without going back to pixels.

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LBADSA

Description

LBADSA is based on the fitting of the Young-Laplace equation to the image data to measure drops.

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DropSnake

Description

DropSnake is based on B-spline snakes (active contours) to shape and measure a drop.

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Protein Array Analyzer for ImageJ

Description

Protein array is used to analyze protein expressions by screening simultaneously several protein-molecule interactions such as protein-protein and protein-DNA interactions. In most cases, the detection of interactions leads to an image containing numerous lines of spots that will be analyzed by comparing tables of intensity values. To describe the observed different patterns of expression, users generally show histograms with the original associated images [1]. The “Protein Array Analyzer” gives a friendly way to exploit this type of analysis, thus allowing quantification, image modeling and comparative analysis of patterns.

The Protein Array Analyzer, which was programmed in ImageJ’s macro language, is an extention of the Dot Blot Analyzer, [2], [3] a graphically interfaced tool that greatly simplifying analysis of dot arrays.

Multi-Template matching

Description

Multi-template matching can be used to localize multiple objects using one or a set of template images.

Contrary to previous implementations that allow to use only one template, here a set of templates can be used or the initial template(s) can be transformed by rotation/flipping.

Multiple objects detection without redundant detections is possible thanks to a Non-Maxima Supression relying on the degree of overlap between detections.

The solution is available as a Fiji plugin (Multi-Template Matching update site) and as a Python package (Multi-Template-Matching on PyPI)

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FPBioimage

Description

FPBioimage is a volumetric visualization tool which runs in all modern web browsers. Try the tool yourself at our example site here.

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