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IMD File Analysis

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Posts: 1

Joined: Mon Jul 28, 2014 3:36 pm

Post Fri Jul 08, 2016 4:56 pm

IMD File Analysis

Hello -

Does anyone have an easy way to extract intensity data from IMD files without processing them through the CyTOF software? I don't want to just see events that are above threshold, I'm interested in looking at all collected data prior to this type of filtering. In particular, I'm interested in looking at mass cytometry data similarly to the way Zunder shows in the 2015 nature protocol barcoding paper (supplementary figure 2). Is there a particular software (i.e. matlab) that is well suited for this kind of data?

Also - can anyone comment on the technical details of the noise reduction option in acquisition parameters?




Posts: 2677

Joined: Fri Nov 01, 2013 5:30 pm

Location: Stanford HIMC, CA, USA

Post Fri Jul 08, 2016 11:33 pm

Re: IMD File Analysis

Hi Heather,

For creating the figures, you might check out the utilities here: https://github.com/nolanlab/MatlabCytof ... master/imd

For technical information on noise reduction, I think you'll have to contact Fluidigm. I *think* it has to do with the noise below the limit of the lower convolution threshold being driven to zero when the option is turned on. However, I just skimmed through manuals all the way back to CyTOFv1, as well as some CyTOF technical papers like the Bandura et al Analytical Chemistry 2009 with no detailed luck.

If you do find out, please post about it! :)


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