BD Pathway - Image Processing

[Joe Trask]

For those using the BD Pathway I would be interested in learning what
post image acquisition processing steps you are using other than
Attovision to interrogate the image. Thanks.

[hpke]

Dear Joe,

If we do not use AttoVision, what we do is the following:
1., Since the images comes in a pretty complicated structure (/plate/
well/images) and in montage, we split them to be able to easier handle
and put to an simpler structure
2., Than we make the image processing (segmentation) e.g.: with
CellProfiler, or with custom MatLab functions, etc
3., Feature extraction (this is really nicely done in CellProfiler)
4., For statistical analysis: Advanced Cell Classifier (ACC) or for
easier readout custom MatLab
5., Post analysis: High Content Data Chain (HCDC), or SpotFire

Hope this helps,
Peter

[Oscar (Joe) Trask]

Dear Peter,

Thank you for the reply. Are you using Attovision or another method to split the images from the larger montage generated from Attovision?

Regards,
Joe
________________________________________
From: highc...@googlegroups.com [highc...@googlegroups.com] On Behalf Of hpke [peter....@lmc.biol.ethz.ch]
Sent: Friday, October 09, 2009 7:58 AM
To: High Content Imaging
Subject: [High Content Imaging] Re: BD Pathway - Image Processing

[Casey Laris]

Hi Joe and Peter,

You might take a look at our CyteSeer software as well. It reads the
BD/Atto formated images directly and goes through what we consider the
standard image cytometry/high-content analysis steps from there:

- cell-by-cell image segmentation
- measure features for arbitrary populations & sub-populations of cells
- report cell & plate level statistics: z', z-score, t-test, counts,
means etc...
- all the numeric data is exportable or directly readable as csv files
for use in other tools as needed
- support for a broad set of images types across arbitrary sets of
fields/colors/plates etc...

I want to be sure to disclose my commercial interest in the product
but it's definitely worth keeping in mind for this kind of question.
There's a free download & full featured trial available online that
should let you get a feel for how well it works for you. We're always
interested in hearing what works and what doesn't.

Best,

Casey Laris
Vala Sciences Inc. | Director of Applications
Voice: 858.461.6862 | Fax: 888.742.1230
www.valasciences.com | cla...@valasciences.com