Cell or particle Counting and scoring stained objects using CellProfiler

This is a jupyther notebook demonstrating the run of a code from IDR data sets by loading a cell profiler Pipeline 

It calls for data directly from the IDR, and can be ran online on a cloud based on a Jupyter Notebook. The example here is applied on real data set, but does not correspond to a biological question . It aims to demonstrates 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 Cell Profiler Pipeline and remove the reading modules from this defaults pipeline.

It creates a csvfile and display it in the notebook.

It makes some plot with matplotlib.