Replace Red with Magenta

Description

This plugin converts all occurrences of red in a red/green image with magenta, effectively replacing it with a magenta/green merge.

Note: the plugin completely ignores the blue channel, and replaces it with a copy of the red channel.

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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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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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SME

Description

Smooth 2D Manifold Extraction (SME).

Three-dimensional fluorescence microscopy followed by image processing is routinely used to study biological objects at various scales such as cells and tissue. However, maximum intensity projection, the most broadly used rendering tool, extracts a discontinuous layer of voxels, obliviously creating important artifacts and possibly misleading interpretation. Here we propose smooth manifold extraction, an algorithm that produces a continuous focused 2D extraction from a 3D volume, hence preserving local spatial relationships. We demonstrate the usefulness of our approach by applying it to various biological applications using confocal and wide-field microscopy 3D image stacks. We provide a parameter-free ImageJ/Fiji plugin that allows 2D visualization and interpretation of 3D image stacks with maximum accuracy.

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SME

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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Filopodyan

Description

Fiji plugin for detecting, tracking and quantifying filopodia

Nuclei Segmentation (ilastik)

Description

NEUBIAS-WG5 workflow for nuclei segmentation using ilastik v1.3.2 and Python post-processing.

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