Bioimage informatics

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

- Unique id for data

Supports sharing and collaboration with access control

- Allows users to upload, view, update or download data based on their access privileges

Supports multiple ways of attaching meta-information

- Annotations, comments and file attachments

-Analysis results as query-able visual objects

Supports Archiving (data moving to another long-term storage but still searchable)

Facilitates custom visualization and analysis

- Access data from preferred analysis and visualization tools

- Access relevant bits of data to build efficient web and mobile application

Facilitate easy access to analysis and visualization applications hosted on other servers

- Run analysis on dedicated compute clusters

- Access applications hosted and published by other users

Highly Scalable

- Supports on-the-fly addition of server nodes to scale concurrent usage

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.

It loads the CellProfiler Pipeline and replace the reading modules used to read local files from this defaults pipeline by module allowing to read data remotely accessible.

It creates a CSV file and displays it in the notebook.

It makes some plot with Matplotlib.

Python is a programming language.

Python 2.7.0 was released on July 3rd, 2010.

Python 2.7 is scheduled to be the last major version in the 2.x series before it moves into an extended maintenance period. This release contains many of the features that were first released in Python 3.1.

 A bugfix release, 2.7.16, is currently available. Its use is recommended.

LibTIFF - TIFF Library and Utilities. This software provides support for the Tag Image File Format (TIFF), a widely used format for storing image data. libtiff is a library, for reading and writing TIFF, a small collection of tools for doing simple manipulations of TIFF images.

Matplotlib is a comprehensive library for creating static, animated, and interactive visualizations in Python.