[ome-users] FLIMfit question

[Munro, Ian]

Hi Kelli

My initial thoughts on this are that, looking at your first, log scale, image you seem to have a significant background.
FLIMfit has 3 options for handling backgrounds :

1) 'Single value' just sets the background used in the fit to a constant set by the user.

2) More realistically ‘image’ allows you to use a background image (just use the same setup w/out a sample)
to cater for spatially-varying backgrounds.

3) Lastly you can use a time-varying background. This is to cater for situations where there is background fluorescence.
For example from the cover-slip.

I’d suggest trying 1) to work out if this is the problem.

Best Wishes

Ian



On 10 Jan 2018, at 20:09, Kelli Fenelon <kelli.fenelon at sickkids.ca<mailto:kelli.fenelon at sickkids.ca>> wrote:

Hi again,

I've attached screenshots and my best attempt at explaining my thought process about the fitting issue I'm having.  Do you think you can help?

Thanks again,

Kelli
________________________________
From: ome-users <ome-users-bounces at lists.openmicroscopy.org.uk<mailto:ome-users-bounces at lists.openmicroscopy.org.uk>> on behalf of Munro, Ian <i.munro at imperial.ac.uk<mailto:i.munro at imperial.ac.uk>>
Sent: January 10, 2018 5:36:05 AM
To: OME User Support List
Subject: Re: [ome-users] FLIMfit question

HI Again Kelli

I was just wondering if any  of my suggestions solved your problems?

Best Wishes

Ian


On 4 Jan 2018, at 16:30, Munro, Ian <i.munro at imperial.ac.uk<mailto:i.munro at imperial.ac.uk>> wrote:

Hi Kelli

Sorry I missed this e-mail earlier.
You can use the Segmentation Manager’s File menu to save and reload segmentations.

Best Wishes

Ian




On 3 Jan 2018, at 22:21, Kelli Fenelon <kelli.fenelon at sickkids.ca<mailto:kelli.fenelon at sickkids.ca>> wrote:

Hi Ian,

That link sends me back to a page that gives me this email address again...

The problem with saving I'm having is that when save as a 'raw' file, it forgets my segmentation.  I guess what I really want to be able to do is save the segmentation.

Thanks again,

Kelli
________________________________
From: ome-users <ome-users-bounces at lists.openmicroscopy.org.uk<mailto:ome-users-bounces at lists.openmicroscopy.org.uk>> on behalf of Munro, Ian <i.munro at imperial.ac.uk<mailto:i.munro at imperial.ac.uk>>
Sent: January 3, 2018 5:01:14 PM
To: OME User Support List
Subject: Re: [ome-users] FLIMfit question

Hi Kelli

Normally the best way to ask questions is via the flimfit-users list http://lists.openmicroscopy.org.uk/mailman/listinfo/flimfit-users<https://urldefense.proofpoint.com/v2/url?u=http-3A__lists.openmicroscopy.org.uk_mailman_listinfo_flimfit-2Dusers&d=DwMGaQ&c=Sj806OTFwmuG2UO1EEDr-2uZRzm2EPz39TfVBG2Km-o&r=7dh5bJkL96w3P1ytEeKLlSJh-HDZau-n0oI2N8-ia1I&m=jlhKZYUaGHQqwUmJkM2FHJu-edlR1HkTxm2JZaao9ig&s=Iqu76w8GRZb3mEFBTZxISm8v5AHmHAKEkaWPcpOI2VY&e=>

I’m not sure about  zooming the segmentation manager.
I’ll investigate and get back to you.

I’m afraid I don’t follow exactly what you mean by saving progress could you please clarify?
In case it helps, you can save your data as a ‘raw’ file File->Save as Raw Dataset... to allow fast reloading.
You can also save the fit results using File->Save ft results table…

Best Wishes

Ian








On 3 Jan 2018, at 19:15, Kelli Fenelon <kelli.fenelon at sickkids.ca<mailto:kelli.fenelon at sickkids.ca>> wrote:

Hi,

I'm not sure if this is the proper method of going about asking my question, but it will have to do whilst my forum account awaits approval.

Is there any way to zoom in the segmentation manager or otherwise?

Is there any way to save my progress and continue later?  (Save fit/half a segmentation/etc)

Thanks a billion,

Kelli

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