Question: Processing imaging data from high throughput compound screen with EBImage
gravatar for phil.chapman
18 months ago by
United Kingdom
phil.chapman120 wrote:


My group are planning to conduct a 15k compound high content biology screen and I'm looking into options for analysing the image data.  We'd probably just be doing a simple cell count and maybe cell size to start with.  Although we have commerical software to do this (Definiens), I'm not sure how well our set-up will scale given the hardware it's on.  Another option is to use our institute's NGS compute cluster, and analyse the data using the Bioconductor package EBImage which I think would scale much better.

In terms of learning resources there's the package vignette and the following tutorial from CSAMA2015, but are there any additional workflow papers or other resources that might be helpful to me in setting this up?




ADD COMMENTlink modified 17 months ago • written 18 months ago by phil.chapman120
gravatar for Wolfgang Huber
18 months ago by
EMBL European Molecular Biology Laboratory
Wolfgang Huber13k wrote:

Hi Phil

It's a good idea to do this with EBImage. We've used it for several imaging-based HT screens. The vignette of the paper  "A Map of Directional Genetic Interactions in a Metazoan Cell" by Bernd Fischer et al. generates all figures in the paper. It has a section on the HT image processing per se (as well as the downstream QA/QC, dimension reduction etc.):

There is also a draft version of a teaching chapter on image data analysis that heavily relies on EBImage, and which I am happy to share (caveat - it's really a draft, forgive the bumps):

Let us know about your experiences or questions that come up. Pull requests or suggestions are also welcome. It would also be interesting to hear what others on this forum use? E.g. there is also (focus on time lapse imaging; interoperable with R through the cellh5 data exchange format (HDF5-based, ), and uses a clever interactive learning approach that maybe helpful if the segmentation is difficult.



ADD COMMENTlink written 18 months ago by Wolfgang Huber13k

Thanks Wolfgang this is exactly the sort of information I was hoping for.

My main issue to start with is how to get the image data out of the commercial software (Perkin Elmer Opera Phenix) in the first place and into an open format.  I naively assumed it would just be a bunch of images but it seems not.  The Open Microscopy Environment project seems to have lots of useful tools as well though so I'm hopeful I'll be able to work my way through this.

ADD REPLYlink written 18 months ago by phil.chapman120

In that case RBioFormats might prove helpful. It provides an R interface to the OME image formats reader, which should allow you to load the data directly into R without the need of intermediate format conversion.

ADD REPLYlink written 18 months ago by Andrzej Oleś670
gravatar for Andrzej Oleś
18 months ago by
Andrzej Oleś670
EMBL Heidelberg, Germany
Andrzej Oleś670 wrote:

Dear Phil,

you can also have a look at the supplemental data packages accompanying the following papers. Each of these packages' vignette contains a description of the image analysis pipeline.




ADD COMMENTlink written 18 months ago by Andrzej Oleś670

This is great thanks Andrzej!

ADD REPLYlink written 18 months ago by phil.chapman120
gravatar for phil.chapman
17 months ago by
United Kingdom
phil.chapman120 wrote:

Some other useful links for posterity:

Earl Glynn's RNotes blog:

Slideset from Wolfgang Huber:

Machine Learning in cell biology - teaching computers to read phenotypes:




ADD COMMENTlink written 17 months ago by phil.chapman120
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