Image Title Category Type Description Updated
need a thumbnail cython Software 09/09/2018 - 22:49
need a thumbnail simpleITK Software 09/09/2018 - 22:49
Rivulet 2 Software Collection 09/09/2018 - 22:49
need a thumbnail ZEN Blue Software 08/22/2018 - 14:55
ZEN Intellesis Trainable Segmentation Software Component, Workflow

Perform Advanced Image Segmentation and Processing across Microscopy Methods
 

08/22/2018 - 14:55
need a thumbnail idr-py Software 08/20/2018 - 11:20
need a thumbnail rOMERO-gateway Software Component

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

08/20/2018 - 10:58
bisque screenshot BisQue Software Collection

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.

08/17/2018 - 17:06
openImadis Openimadis Software Component

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

08/17/2018 - 16:45
scientifig ScientiFig Software Component

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.

08/17/2018 - 15:09
Fit a model for the growth of yeast cells Software Workflow

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'.

08/20/2018 - 11:24
Positivepercentcell Cell or particle counting and scoring the percentage of stained objects Software Workflow

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. 

08/16/2018 - 13:49
jupyter Cell or particle Counting and scoring stained objects using CellProfiler Software Workflow

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.

08/20/2018 - 11:20
Combined view from Figure 1 Lawo et al. Quantification of outer ring diameters of centriole or PCM proteins of cycling HeLa cells in interphase Software Workflow

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.

08/20/2018 - 11:11
Scientific Community Image Forum Forum

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.

 

08/06/2018 - 13:52
need a thumbnail pystackreg Software Component

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.

08/07/2018 - 13:41
Detection of Molecules - DoM Software Collection

A collection of components for super resolution image data:

  • Detect Molecules
  • Reconstruct Image
  • Results table
  • Drift correction
  • Chromatic correction
06/29/2018 - 12:27
https://aivia.wikispaces.com/Welcome+to+the+Aivia+Wiki Training Material 06/28/2018 - 02:31
Aivia Software Collection, Workflow 06/28/2018 - 02:31
need a thumbnail JDK Software 06/06/2018 - 15:16