Image Title Category Type Description Updated
DragonFly DragonFly Software Collection

Dragonfly is a software platform for the intuitive inspection of multi-scale multi-modality image data. Its user-friendly experience translates into powerful quantitative findings with high-impact visuals, driven by nuanced easy-to-learn controls.

For segmentation: It provides an engine fior machine Learning, Watershed and superpixel methods, support histological data .

It offers a 3D viewer, and python scripting capacities .

It is free for reserach use, but not for commercial usage.

10/17/2019 - 12:18
CSIRO science image library Dataset

collection of real life science images and videos from australian research labs.

including photographs of plants, microscopy equipments, microscopy images

08/08/2019 - 15:54
Neuroglancer Neuroglancer Software Component

Web based viewer developped for google for very big data: 

Neuroglancer is a WebGL-based viewer for volumetric data. It is capable of displaying arbitrary (non axis-aligned) cross-sectional views of volumetric data, as well as 3-D meshes and line-segment based models (skeletons). The segmentation has to be done before loading the dataset, it is not done Inside the viewer.

This is not an official Google product.

It has among other the nice feature of beeing able to generate url for sharing a specific view.

Note that the only supported browser for now are 

08/13/2019 - 10:54
Breast Cancer Histopathological Database (BreakHis) Dataset

2,480  benign and 5,429 malignant annotated histophatology dataset of cancer breast tissue from 82 patients

using different magnifying factors (40X, 100X, 200X, and 400X)

07/26/2019 - 16:25
need a thumbnail 3D-Segmentation Software Workflow

Image removed.

06/21/2019 - 14:40
need a thumbnail ImageJFIJI Software Workflow

The research goal of this paper was to provide unbiased counts of labeled astrocytes and to estimate the area they cover, further to develop tools for defining the orientation of coupling within astrocyte networks under different stimuli.

06/21/2019 - 14:13
WormScan Software Collection

We have developed WormScan, an automated image acquisition system that allows quantitative analysis of each of these four phenotypes on standard NGM plates seeded with E. coli. This system is very easy to implement and has the capacity to be used in high-throughput analysis.

10/15/2019 - 10:59
ikosa Ikosa Software Collection

online image data management system which supports authenticated image upload, cloud-based storage, project-based management and viewing of standard and whole slide images. One can use different annotation tools to highlight important objects or areas within images. It is the first basic version and new features such as sharing for easy collaboration with your colleagues or first automated analysis applications based on artificial intelligence will be added soon.

Ikosa Portal: multi user image data management

10/16/2019 - 11:13
Protein Array Analyzer for ImageJ Software Collection

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.

05/17/2019 - 15:58
Zebrafish larvae - Widefiled/Brightfield Dataset

Datasets originate from internal test runs at ACQUIFER on the Imaging Machine (see also application note on "The ACQUIFER PlateViewer: A tool for visualizing high content screening data and supervised feedback microscopy")

04/29/2019 - 12:22
Preview Medaka embryo in 96 well plate - Widefield Brightfield Dataset

102 hpf medaka embryos in 96 well plate (4 embryo/well) - brightfield - 2X magnification - ACQUIFER Imaging Machine

Gierten, Jakob, et al. "Automated high-throughput heart rate measurement in medaka and zebrafish embryos under physiological conditions." bioRxiv (2019): 548594.

Used as benchmark dataset for Multi-Template-Matching by Thomas and Gehrig 

See implementation in Fiji https://github.com/LauLauThom/MultipleTemplateMatching

04/29/2019 - 12:20
need a thumbnail Multi-Template matching Software Component

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.

07/29/2019 - 08:56
FPBioimage Software Collection

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

04/18/2019 - 15:24
PYME Software Collection

The PYthon Microscopy Environment is an open-source package providing image acquisition and data analysis functionality for a number of microscopy applications, but with a particular emphasis on single molecule localisation microscopy (PALM/STORM/PAINT etc ...). The package is multi platform, running on Windows, Linux, and OSX.

It comes with 3 main modules:

  • PYMEAcquire - Instrument control and simulation
  • dh5view - Image Data Analysis and Viewing
  • VisGUI - Visualising Localization Data Sets
04/14/2019 - 16:08
Spatiotemporal quantification of monolayer cell migration Training Material

MATLAB, for advanced analysts. Slides, Scripts, Reproduction of results & deconstruction. Uniquely designed analtical approaches towards understanding cell cluster movements, based on stress / cell migration analysis.

04/08/2019 - 14:42
Filopodyan Software Collection

Fiji plugin for detecting, tracking and quantifying filopodia

04/19/2019 - 17:01
Analysis of filopodia dynamics Training Material

ImageJ & R, for advanced analysts. Slides, Scripts, Reproduction of results & deconstruction. Segmentation of filopodia (thin filamentous structure) and analysis of their shape and movements to characterize phenotypes.

04/08/2019 - 14:36
High Content Image data Screening and Analysis Training Material

MATLAB, CellProfiler, Advanced Cell Classifier, for advanced analysts. Slides, Scripts, Reproduction of results & deconstruction. We aim to implement an image-based analysis of a biological system by profiling the phenotipic response of a cancer cell line following perturbation with a small-molecule compound library

04/08/2019 - 14:21
Stitch Tiles, Flat Field Correction, Quantify ProtX intensity at Nuclei Training Material

ImageJ, for those with GUI knowledge but without scripting knowledge

04/08/2019 - 14:17
Introduction to ImageJ macros: Quantify the enrichment of NPC proteins at the nuclear envelope, relative to its cytoplasmic localisation Training Material

ImageJ, for those with GUI knowledge but without scripting knowledge

04/08/2019 - 14:14