PhenoRipper

Cite PhenoRipper in publications

• How to cite PhenoRipper in publications?
  To cite PhenoRipper in your publication, use the following:
  
  Satwik Rajaram, Benjamin Pavie, Lani F Wu & Steven J Altschuler,
  PhenoRipper: software for rapidly profiling microscopy images
  Nature Methods | Vol. 9 No. 7 | July 2012 | 635-637
  (hide)

Platform Support

• Will you support other operating systems?
  Yes, we will release soon a Linux 32 and 64 bit version. We are just waiting to find the best way to package it!
  (hide)
• Do you distribute the source code?
  Yes, we distribute the source code on our Github repository under the GPL licence. To clone it, install Git and type:

  git clone https://github.com/awlab/phenoripper.git

  (hide)

Data Format

• What image formats do you support?
  Right now we can process all image formats supported by MATLAB TIFF/STK/PNG/... (see a full list here)
  (hide)

Data Export

• Can I export the result of the phenoripped data?
  To export any figures (MDS Plot, Clustergram, etc...) or the result of the features, from the PhenoBrowser, select Export on the Menu bar then select what you want to export (Data export the raw data after processing.):
  (hide)

Algorithm

• Is PhenoRipper Supervised?
  PhenoRipper does not perform supervised classification. By default, when PhenoRipper compares microscopy images, it does not use prior information about the experimental conditions underlying the data. However, users have the option to allow PhenoRipper to make use of experimental annotation in two ways:
  
  1-Displaying results: The scatter plots of profiles in PhenoBrowser can be grouped, colored, or labelled based on user annotation. This visualization helps users explore and interpret the results produced by PhenoRipper, even though the annotation itself is not used during the analysis.
  
  2-Subsampling data: To identify stereotypical block types (the features used in profiling and comparing images), PhenoRipper analyzes a random subset of blocks selected from a random subset of all images. The user has the option to bias this default behavior by telling PhenoRipper which sets of images could be considered as replicates. This option can be useful when the user choses to subset only a very small number of images and wants to avoid redundant sampling.
  (hide)

Other Image Analysis Tools

• There are many existing image analysis software tools. Here is a very incomplete list to help get you started. We are happy to add more links – just let us know!
  • CellProfiler : http://www.cellprofiler.org/
  • iCluster : http://icluster.imb.uq.edu.au/
  • ImageJ : http://rsbweb.nih.gov/ij/
  • wnd-charm : http://code.google.com/p/wnd-charm/
  (hide)

Who We Are

We investigate the role of cellular heterogeneity in mammalian physiology and disease. Our investigations tightly couple experiment, image-based analysis, and mathematical modeling.