ROI 1-click tools for ImageJ/Fiji

Description

This macro toolset offers additional click tools for the rapid annotations of ROI in ImageJ/Fiji.

The ROI 1-click tools can be setup with a predefined shape, and custom actions to perform upon click (Add to ROI Manager, Run Measure, Go to next slice, run a macro command...)

To install in Fiji, just activate the ROI 1-click tools 

ImageM

Description

ImageM integrates into a GUI several algorithms for interactive image processing and analysis. Interface is largely inspired from the open source software "ImageJ".

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StarDist - ImageJ

Description

This is the ImageJ/Fiji plugin for StarDist, a cell/nuclei detection method for microscopy images with star-convex shape priors ( typically for Dapi like staining of nuclei). The plugin can be used to apply already trained models to new images.

Stardist

DeepImageJ

Description

DeepImageJ is a user-friendly plugin that enables the use of a variety of pre-trained deep learning models in ImageJ and Fiji. The plugin bridges the gap between deep learning and standard life-science applications. DeepImageJ runs image-to-image operations on a standard CPU-based computer and does not require any deep learning expertise.

Training developper constructs and upload trained model, and made them available to users.

Models are available in a repository here https://deepimagej.github.io/deepimagej/models.html

It is macro recordable. It is advised to luse DeepImageJ on a computer with GPU (CPU will likely be 20x slower)

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deepImageJ

MorphoNet Python API

Description

The Morphonet Python API provide an easy interface to interact directly with the MorphoNet server. Very useful to upload, download your dataset and superimpose on it any quantitative and quantitative informations.

Spot Detection Dmap (ImageJ)

Description

This workflow detects spots in a 2D image by filtering the image by Laplacian of Gaussian (user defined radius), thresholding (user defined threshold) and finding local intensity maxima in mask distance map (Dmap).

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NucleusJ

Description

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Starting from image stacks, the nuclear boundary as well as nuclear bodies are segmented. As output, NucleusJ automatically measures 15 parameters quantifying shape and size of nuclei as well as intra-nuclear objects and the positioning of the objects within the nuclear volume.

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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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