Contents

Perform Advanced Image Segmentation and Processing across Microscopy Methods
 

R wrapper around the OMERO Java Gateway, to enable access to OMERO via R using rJava

Bisque (Bio-Image Semantic Query User Environment) : Store, visualize, organize and analyze images in the cloud. It also allow to run workflows using a set of deployed tools, such as CellProfiler, RootTipMultin Nuclear Tracker, Microtubule tracker etc...

Bisque was developed for the exchange and exploration of biological images.

OpenImadis stands for Open Image Discovery: A platform for Image Life Cycle Management. It was previously called CID iManage (for Curie Image Database).

No image data conversions, no duplication.

- Uploads data to a secure server in the original format

ScientiFig is a free tool to help you create, format or reformat scientific figures. It comes either as a stand alonesoftware, either as a Fiji/IJ plugin.

This notebook uses the rOMERO-gateway and EBImage to process an Image associated to the paper 'Timing of gene expression in a cell-fate decision system'.

This one example workflow from the Cell Profiler(CP)  Examples . CP is commonly used to count cells or other objects as well as percent-positives, by measuring the per-cell staining intensity. This pipeline shows how to do both of these tasks, and demonstrates how various modules may be used to accomplish the same result. 

This is a Jupyter notebook demonstrating the run of a code from IDR data sets by loading a CellProfiler Pipeline 

The example here is applied on real data set, but does not correspond to a biological question. It aims to demonstrate how to create a jupyter notebook to process online plates hosted in the IDR.

It reads the plate images from the IDR.

This workflow can be ran with data from 3D-SIM showing the centrosomes in order to compare the distribution of diameters of rings (or toroids) of different proteins from the centrioles or the peri centriolar material. It aims to reproduce the results of the Nature Cell Biology Paper Subdiffraction imaging of centrosomes reveals higher-order organizational features of pericentriolar material  from the same data set but with a different analysis method.

The Image.sc forum focuses on software-oriented aspects of scientific imaging, particularly (but not limited to) image analysis, processing, acquisition, storage, and management of digital scientific images. The primary objective is to foster independent learning for everyone in the community.

Python/C++ port of the ImageJ extension TurboReg/StackReg written by Philippe Thevenaz/EPFL.

A python extension for the automatic alignment of a source image or a stack (movie) to a target image/reference frame.

A collection of components for super resolution image data:

• Detect Molecules
• Reconstruct Image
• Results table
• Drift correction
• Chromatic correction