Image Title Category Type Description Updated
Replace Red with Magenta Software Component

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.

11/12/2019 - 00:13
need a thumbnail Napari image viewer Software Component

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.

11/08/2019 - 10:22
need a thumbnail OligoMacro Toolset Software Workflow

OligoMacro Toolset, is an ImageJ macro-toolset aimed at isolating oligodendrocytes from wide-field images, tracking isolated cells, characterizing processes morphology along time, outputting numerical data and plotting them. It takes benefit of ImageJ built-in functions to process images and extract data, and relies on the R software in order to generate graphs.

10/27/2019 - 21:44
need a thumbnail MATLAB Wavelet toolbox Software Collection 10/18/2019 - 18:39
automated structures analysis program (ASAP) Software Workflow

ASAP allows to automatically detect, classify and quantify structures acquired by super resolution microscopy. 

10/18/2019 - 13:10
need a thumbnail Icy Spot Tracking Software Component

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

10/18/2019 - 13:17
need a thumbnail Icy Label Extractor Software Component 10/17/2019 - 16:56
need a thumbnail Image registration in Matlab with Image Processing Toolbox Software Collection, Component

Align two images using intensity correlation, feature matching, or control point mapping

Together, Image Processing Toolbox™ and Computer Vision Toolbox™ offer four image registration solutions: interactive registration with a Registration Estimator app, intensity-based automatic image registration, control point registration, and automated feature matching. 

10/17/2019 - 13:49
Adaptive Pixel Representation Software Collection

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.

10/16/2019 - 18:01
Mathematica Software Collection

Wolfram Mathematica (usually termed Mathematica) is a modern technical computing system spanning most areas of technical computing — including neural networksmachine learningimage processinggeometrydata science

10/16/2019 - 14:51
LBADSA Software Component

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

10/16/2019 - 13:24
DropSnake Software Component

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

10/16/2019 - 13:20
FastSME Software Component

FastSME: Faster and Smoother Manifold Extraction From 3D Stack.

10/15/2019 - 15:47
SME SME Software Component

Smooth 2D Manifold Extraction (SME).

10/15/2019 - 13:36
Introduction to R for bioimage analysis Training Material

This session covers the basics of the R programming language in the context of a bioimage analysis workflow. It aims at getting started with the analysis of data extracted from one or several images, here tracking data. Tracking data were extracted using the Fiji plugin TrackMate and are available in /datasets/fly_embryo/.

09/10/2019 - 22:17
Deep Learning from scratch Training Material

Make your first experience with TensorFlow-Keras

Part 1 :


Part 2 :


Part 3 :


08/29/2019 - 10:22
Fairsharing FAIRsharing Eurobioimaging collection Dataset

FAIRsharing is a database of databases and repositories. The collection gathered by EuroBioImaging contains alist of public database hosting images from biomedical siences. They are classified using a taxonomy for the biological model used (Homo Sapiens, Drosophila,...)

08/26/2019 - 14:38
deepcell DeepCell Software Component


DeepCell is neural network library for single cell analysis, written in Python and built using TensorFlow and Keras.

DeepCell aids in biological analysis by automatically segmenting and classifying cells in optical microscopy images. This framework consumes raw images and provides uniquely annotated files as an output.

The jupyter session in the read docs are broken, but the one from the GitHub are functional (see usage example )

08/26/2019 - 12:30
mosaick muscle cross-sections Dataset

Muscle cross-section with immunofluorescence , to count myofibers

08/26/2019 - 11:59
embryo DIC Mouse embryos Dataset

Fluorescence microscopy cannot be used to image human embryos to determine embryo viability for in vitro fertilization because the introduction of exogenous fluorescent dyes is considered a toxic procedure. As a result, embryo viability has been measured primarily using differential interference contrast (DIC).

08/26/2019 - 11:49