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IMD file conversion

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dahern

Participant

Posts: 12

Joined: Tue Mar 31, 2015 3:45 pm

Post Fri Sep 09, 2016 1:22 pm

IMD file conversion

Hi all,

I'm trying to convert some IMD files to text files (and then on to FCS) using the CyTOF software. The size of the text files after conversion however are huge, along with the subsequent FCS files. Far too big to be of use.

As an example one IMD file is 468, 014 KB and when I convert to text using the software the resulting file is 800,124 KB (The conversion done originally by the software directly after acquisition resulted in a text file of 1,288 KB).

Couple of questions - Does this sound correct or am I doing something wrong and why the drastic difference in the size of the text file when the software converts automatically at the end of acquisition (1,288 KB) to the size of file resulting when I manually convert using the CyTOF software (800,124 KB).

Thanks!

David.
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dahern

Participant

Posts: 12

Joined: Tue Mar 31, 2015 3:45 pm

Post Fri Sep 09, 2016 2:43 pm

Re: IMD file conversion

Just an update to this. Using the "analysis" tab instead of the "convert IMD" tab I get a text file of 1,341 KB and an FCS file of 1,293 KB - pretty similar to size of files created by the software at the end of the acquisition run (FCS file is the identical size).

So I guess the convert IMD function is different to the analysis function and I've been using it incorrectly?
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mleipold

Guru

Posts: 2086

Joined: Fri Nov 01, 2013 5:30 pm

Location: Stanford HIMC, CA, USA

Post Fri Sep 09, 2016 3:08 pm

Re: IMD file conversion

Hi David,

Could you tell us which instrument model you're using, and which version of software?

Are you reprocessing the IMDs because you're changing default parameters?


Mike
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dahern

Participant

Posts: 12

Joined: Tue Mar 31, 2015 3:45 pm

Post Fri Sep 09, 2016 3:12 pm

Re: IMD file conversion

Hi Mike,

I'm still on a CyTOF 1 and using the old software - version 5.1.648

I'm doing the conversion because we've had a few files recently that didn't convert automatically after acquisition - not sure if this is a storage space issue or not.

For the conversion I've been using the default parameters on the software.

David.
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mleipold

Guru

Posts: 2086

Joined: Fri Nov 01, 2013 5:30 pm

Location: Stanford HIMC, CA, USA

Post Fri Sep 09, 2016 3:56 pm

Re: IMD file conversion

Hi David,

From the v1 manual I have, I attached a PDF of what I think you're talking about:
page 1: IMD
page 2: Analysis

If you are wanting to make FCS files from your IMD file, you want to use Analysis.

If I understand the "IMD" one correctly, it's converting your entire IMD file into a text file, *not just* your cell events. That's why the files are so big.


Mike
Attachments
IMD and Analysis.pdf
(192.8 KiB) Downloaded 276 times
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dahern

Participant

Posts: 12

Joined: Tue Mar 31, 2015 3:45 pm

Post Mon Sep 12, 2016 12:18 pm

Re: IMD file conversion

Thanks Mike, that explains it. I misunderstood completely what the IMD file conversion tool was for.

David.
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Dominique

Participant

Posts: 1

Joined: Fri Nov 23, 2018 4:59 pm

Post Mon May 27, 2019 9:37 am

Re: IMD file conversion

In the context of imd conversion, I would like to ask another question.
When restoring .fcs from .imd (imd processing) with the CyTOF software (6.5 or 6.7), the resulting .fcs file is showing an aberrant acquisition time when opened in FlowJo 10. For example, an acquisition time of 4000 seconds will be multiplied by 1000 or even 1000 000.
This modified time scale is having consequences on downstream processing of the data (i.e: normalization)
One was maybe already confronted to this problem. Thank you in advance for your help.
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mleipold

Guru

Posts: 2086

Joined: Fri Nov 01, 2013 5:30 pm

Location: Stanford HIMC, CA, USA

Post Tue Aug 13, 2019 5:45 pm

Re: IMD file conversion

Hi Dominique,

It's a couple months since you posted about this, but CyTOF TIME parameter isn't in seconds, it's in milliseconds: see thread here: viewtopic.php?f=3&t=1546

Are you saying that an FCS file you get from IMD re-processing gives a different TIME scale than a regular FCS file that you get from a regular sample acquisition? If so, that's odd, because that shouldn't happen....


Mike

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