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missing gaussian parameters?

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rgrenfell

Contributor

Posts: 30

Joined: Thu Aug 27, 2015 12:31 pm

Post Thu Aug 22, 2019 2:33 pm

missing gaussian parameters?

Hi everyone

the last few days of running has just shown up to us that we are missing the 4 gaussian parameters from the .FCS files

looks like it happened around the same time as a service visit on the Helios. Our fcs files from before the visit are ok, but the ones after are missing the 4 parameters

Anyone got any ideas about what settings (& where) an engineer (or us, if it's possilble) would have changed, for us to be able to get those back again.
I hope that they will still be generatable from the .IMD

Any ideas?
(also chasing this up with Fluidigm, but holiday time means they are a little light on people here at the moment)

Thanks
Richard
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DMcDonald

Contributor

Posts: 21

Joined: Thu Nov 26, 2015 10:14 am

Post Thu Aug 22, 2019 2:49 pm

Re: missing gaussian parameters?

Hi Richard,

Have you been getting any errors e.g. Guassian discrimination failed during FCS conversion?

There's a check box for guassian discrimination within the templates "advanced" tab, perhaps check to see if that is unchecked? Final check box beneath preserve IMD etc...

Best wishes,
David
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mleipold

Guru

Posts: 5796

Joined: Fri Nov 01, 2013 5:30 pm

Location: Stanford HIMC, CA, USA

Post Thu Aug 22, 2019 2:52 pm

Re: missing gaussian parameters?

Hi Richard,

Did the engineer install the new software update during this service call? Fluidigm announced a new software release at the UGM in June (compatible with WIndows 10, which will make our IT department happier....), and I think they're starting the installs on that.

For reference: we have *not* gotten the installation yet, so we're still running the older v6.7.1014 (you can see it at the login prompt before the software opens).


Wouldn't be the first time Fluidigm has made software changes..................


Mike
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rgrenfell

Contributor

Posts: 30

Joined: Thu Aug 27, 2015 12:31 pm

Post Thu Aug 22, 2019 4:03 pm

Re: missing gaussian parameters?

an update:

thanks everyone for suggestions.
We'd checked the template, all was fine, the fcs generation still had the gaussian option ticked.

Fluidigm have remoted in, and have been looking at the java path in the control panel, which wasnt pointing at java now (and java seems to be missing - got to chase that up with IT here in case they have done something network wise)

so, once the fcs genarator is now looking at java properly, we can re-do our fcs files, and they now have their extra parameters

thanks everyone
Richard
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dtdavani

Participant

Posts: 12

Joined: Fri Sep 11, 2015 9:52 pm

Post Thu Aug 22, 2019 4:13 pm

Re: missing gaussian parameters?

Hi All,
I hope this is not to late! Back in the day when I was at Toronto SickKids core we had the same problem ( I miss CYTOF challenges;).
This happens when the windows JAVA is updated CYTOF software cannot find it's default JAVA. here is the solution Fluidigm kindly provided us. I hope it works. Sorry pics did not copy so I have attached the PDF.


loos of Guassian distribution parameters:
This is caused by Java problem (Windows’ Java update)




Do not update Java on Helios computers. If happens:

• To add Gaussian discrimination parameters, you will need to have the IMD files for the acquisitions and you will need the correct Java path on the computer you are processing this. Please disable automatic Java updates if it is enabled, as the Java path in the instrument software is not automatically updated.

• Follow these steps:

• Click on the Process Tab.
• Click on IMD reprocessing. This window will open:

• In Source file, load the IMD file that you wish to convert.
• Ensure that the Gaussian Discrimination checkbox is checked:

• Also make sure that the Lower Convolution Threshold value matches with the one in the template with which the file is acquired. You can find that information in Experiment Manager once you load up the template (enable Advanced settings):


Once ready, click Start in the IMD processing window. The FCS will start being generated.
Attachments
Tips and Tricks.pdf
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