Type
Author
Open Microscopy Environment
Execution Platform
Implementation Type
Programming Language
Supported image dimension
Interaction Level
License/Openness
Description

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'.

The Image "Pos22" is taken from the dataset idr0040-aymoz-singlecell/experimentA/YDA306_AGA1y_PRM1r_Mating. It is a timelapse Image with 42 timepoints separated by 5 minutes. This Image is used to fit a model for the growth of the yeast cells. The notebook does not replicate any of the analysis of the above mentioned paper.

Its purpose is mainly to demonstrate the use of Jupyter and jython with EBimage.

 

What it does:

  • For each time point of one movie:
    • Read the image for this time point  from the IDR
    • Threshold the images and count the cells using ebimage functions
  • Fit an exponentional model to the count of cells against time to get a coefficient of grow (exponential factor)

 

 

 

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