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Custom FCS keywords in Helios software

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vtosevski

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Location: Zurich, Switzerland

Post Wed Sep 11, 2019 12:37 pm

Custom FCS keywords in Helios software

Hi everyone,

Does anyone know if it's possible to save custom keywords into the FCS files during the acquisition at the Helios system? This was possible on some flow cytometers so I was wondering if a similar possibility exists for Helios?

Thanks,
Vinko
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mleipold

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Joined: Fri Nov 01, 2013 5:30 pm

Location: Stanford HIMC, CA, USA

Post Wed Sep 11, 2019 2:43 pm

Re: Custom FCS keywords in Helios software

Hi Vinko,

I'm not aware of any way to do that during regular Helios acquisition.

You can of course add your own keywords in FlowJo/etc after the fact, but I'm not aware of any way to "customize" using the Fluidigm software itself.


Mike
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dtelad11

Master

Posts: 129

Joined: Mon Oct 31, 2016 6:26 pm

Post Wed Sep 11, 2019 2:54 pm

Re: Custom FCS keywords in Helios software

Out of curiosity, how would you like to use the custom keywords?
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mleipold

Guru

Posts: 5796

Joined: Fri Nov 01, 2013 5:30 pm

Location: Stanford HIMC, CA, USA

Post Wed Sep 11, 2019 4:22 pm

Re: Custom FCS keywords in Helios software

Hi El-ad,

Among other things, adding information like which machine was used to acquire a particular sample would be helpful for transparency purposes.

For example, Stanford HIMC has 3 Helios instruments. Being able to add a keyword of "Helios1"/"Helios2"/"Helios3" would be nice. Currently, the Helios *.FCS header lists "Helios" and the software version, but doesn't include the serial number of the instrument:

FCS3.0 98 3595 3596 3595315 0 0 3595316 10961822/$CYT/DVSSCIENCES-CYTOF-6.7.1014/$CYTSN/Helios/


Similarly, people might want to include Plate number, or any other thing they might want to track. I usually include this in the filename, but that results in very long file names. That can cause problems with file path length, etc.


Mike
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dtelad11

Master

Posts: 129

Joined: Mon Oct 31, 2016 6:26 pm

Post Wed Sep 11, 2019 4:27 pm

Re: Custom FCS keywords in Helios software

Understood. Would adding these to the files themselves be superior to tracking it in an external database? Combining the data back (for meta-analysis, for example) would be tricky.
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mleipold

Guru

Posts: 5796

Joined: Fri Nov 01, 2013 5:30 pm

Location: Stanford HIMC, CA, USA

Post Wed Sep 11, 2019 4:39 pm

Re: Custom FCS keywords in Helios software

At least for instrument identification, yes, I think it would be superior to have it written to the file itself.


For other things like Plate: there are advantages to having something contained within a file itself (rather than even in the filename). It's less likely to be accidentally lost or altered: at least in FlowJo, most keywords are "hidden" unless you add them to the displayed columns in your workspace. You can delete keywords, but again, it's not something you can easily do by accident.

Additionally: your external database idea only applies if you and your team are the only ones analyzing those files. If you are published a dataset, yes, ideally you would published metadata documents describing the files (plate, Case vs Control, etc). However, I have to be honest: a lot of people don't, or do a poor job of describing.........most people just dump a bunch of files and call it done. If that info in captured in the FCS header as keywords, it's still attached to the files.


Mike
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vtosevski

Contributor

Posts: 44

Joined: Wed Nov 20, 2013 12:50 pm

Location: Zurich, Switzerland

Post Sun Sep 29, 2019 9:18 pm

Re: Custom FCS keywords in Helios software

Hi both,

Sorry for dropping out, the oh-too-common bandwidth problems...

I have used custom keywords in the past as a way to carry experimental metadata along, such as treatments, groups, etc. Makes later analysis so much easier. I am now writing a lot of those in the filename itself and getting it from there, but custom keywords are much more elegant and error-safe.

I would also like to use those to denote acquisition features like cone used, nebulizer used, etc, bits I am currently manually collecting in the list (also as Mike mentioned, instrument's serial number). As we're now going more and more into regulated domain and many things impact the instrument response, I would use custom keywords to collect also instrument settings like current, MG etc.

Vinko
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dtelad11

Master

Posts: 129

Joined: Mon Oct 31, 2016 6:26 pm

Post Sun Sep 29, 2019 10:42 pm

Re: Custom FCS keywords in Helios software

For what it's worth (and I know this is different than the motivation in the original question), most of the analysis platforms out there allow you to indicate these in the software -- FlowJo, Cytobank, and Astrolabe all have that functionality (see https://youtu.be/ROESqNkWby0 for the Astrolabe experiment setup tutorial as an example).

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