FLIM raw data from SP8 Falcon?

[Petro]

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Hi everybody.
Can I get somehow raw  FLIM data from lif file of SP8 Falcon Leica?
Thanks.
Petro

[Michelle Digman]

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Dear Petro,

There is a converter in the Leica software that allows you to convert the
lif files to "ptu" files and this is the raw data. Try it and let me know
if it works.
Best,
Michelle

*******************************
Michelle A. Digman
Associate Professor
Co-Equity Advisor for the Henry Samueli School of Engineering
BME Associate Chair for Graduate Affairs
Department of Biomedical Engineering
University of California Irvine
<[hidden email]>3103 Natural Sciences II
*http://faculty.sites.uci.edu/digmanlab/
<http://faculty.sites.uci.edu/digmanlab/>*
email: [hidden email]
phone: [phone]
fax: [phone]



On Wed, Sep 2, 2020 at 9:56 AM Khoroshyy Petro <[hidden email]> wrote:

> *****
> To join, leave or search the confocal microscopy listserv, go to:
> http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy
> Post images on http://www.imgur.com and include the link in your posting.
> *****
>
> Hi everybody.
> Can I get somehow raw  FLIM data from lif file of SP8 Falcon Leica?
> Thanks.
> Petro
>

[Petro]

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Dear Michelle.
Thanks.
I will try to find it and let you know the result.
Best regards.
Petro.


On Wed, Sep 2, 2020, 8:27 PM Michelle Digman <[hidden email]> wrote:

> Dear Petro,
>
> There is a converter in the Leica software that allows you to convert the
> lif files to "ptu" files and this is the raw data. Try it and let me know
> if it works.
> Best,
> Michelle
>
> *******************************
> Michelle A. Digman
> Associate Professor
> Co-Equity Advisor for the Henry Samueli School of Engineering
> BME Associate Chair for Graduate Affairs
> Department of Biomedical Engineering
> University of California Irvine
> <[hidden email]>3103 Natural Sciences II
> *http://faculty.sites.uci.edu/digmanlab/
> <http://faculty.sites.uci.edu/digmanlab/>*
> email: [hidden email]
> phone: [phone]
> fax: [phone]
>
>
>
> On Wed, Sep 2, 2020 at 9:56 AM Khoroshyy Petro <[hidden email]>
> wrote:
>
>> *****
>> To join, leave or search the confocal microscopy listserv, go to:
>> http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy
>> Post images on http://www.imgur.com and include the link in your posting.
>> *****
>>
>> Hi everybody.
>> Can I get somehow raw  FLIM data from lif file of SP8 Falcon Leica?
>> Thanks.
>> Petro
>>
>

[Petro]

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Dear Michelle.
Could you tell me the file name for this converter?
I look through all exe files inside of the LAS X folder but I can't find it.
Thanks.
Petro.


On Wed, Sep 2, 2020, 8:27 PM Michelle Digman <[hidden email]> wrote:

> Dear Petro,
>
> There is a converter in the Leica software that allows you to convert the
> lif files to "ptu" files and this is the raw data. Try it and let me know
> if it works.
> Best,
> Michelle
>
> *******************************
> Michelle A. Digman
> Associate Professor
> Co-Equity Advisor for the Henry Samueli School of Engineering
> BME Associate Chair for Graduate Affairs
> Department of Biomedical Engineering
> University of California Irvine
> <[hidden email]>3103 Natural Sciences II
> *http://faculty.sites.uci.edu/digmanlab/
> <http://faculty.sites.uci.edu/digmanlab/>*
> email: [hidden email]
> phone: [phone]
> fax: [phone]
>
>
>
> On Wed, Sep 2, 2020 at 9:56 AM Khoroshyy Petro <[hidden email]>
> wrote:
>
>> *****
>> To join, leave or search the confocal microscopy listserv, go to:
>> http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy
>> Post images on http://www.imgur.com and include the link in your posting.
>> *****
>>
>> Hi everybody.
>> Can I get somehow raw  FLIM data from lif file of SP8 Falcon Leica?
>> Thanks.
>> Petro
>>
>

[Stanislav Vitha-2]

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*****

Hi Petro,
when you are in the FALCON program window (not the regular SP8 imaging panel) or just run the FALCON module offline ("LAS_X_SingleMoleculeDetection.exe" in the BIN  folder of LASX installation), go to File - Export Raw Data.
There you have the option to export as PicoQuant .ptu, Picoquant .pt3  or Picoquant FLIM binary files, .bin)


I would be interested to hear what software the general non-physicist public uses for off-line analysis of the FALCON FLIM data besides the Leica software. I started looking at FlimFit  and SimFCS, but do not quite know what I am doing yet.
I would like to be able to list an affordable option for our core facility users who do not have a Leica LASX license.

Stan

Stanislav Vitha
Microscopy and Imaging Center
Texas A&M University

[Petro]

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Hi Stan.
Thanks for info.
Right now I got some problems with PC. I will try it once I fix it.
As for now I do not know what I will use for analysis. Usually I use python
but I suspect my routines written for spectroscopy will need tuning to work
faster.
Best.
Petro.


On Thu, Sep 3, 2020, 6:50 PM Stanislav Vitha <[hidden email]> wrote:

> *****
> To join, leave or search the confocal microscopy listserv, go to:
> http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy
> Post images on http://www.imgur.com and include the link in your posting.
> *****
>
> Hi Petro,
> when you are in the FALCON program window (not the regular SP8 imaging
> panel) or just run the FALCON module offline
> ("LAS_X_SingleMoleculeDetection.exe" in the BIN  folder of LASX
> installation), go to File - Export Raw Data.
> There you have the option to export as PicoQuant .ptu, Picoquant .pt3  or
> Picoquant FLIM binary files, .bin)
>
>
> I would be interested to hear what software the general non-physicist
> public uses for off-line analysis of the FALCON FLIM data besides the Leica
> software. I started looking at FlimFit  and SimFCS, but do not quite know
> what I am doing yet.
> I would like to be able to list an affordable option for our core facility
> users who do not have a Leica LASX license.
>
> Stan
>
> Stanislav Vitha
> Microscopy and Imaging Center
> Texas A&M University
>

[Deborah Barkauskas]

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Hi Petro and Stan,

This is such a timely post because I just emailed my local Leica specialist a similar question about the .lif format so I can extract the raw data from the .lif file. I currently export each image by hand in the Leica FLIM software as described by Stan. This in itself can take hours depending on the imaging. I am looking for a better way to extract the data I need for analysis.

I then run that data through FLIMFit for lifetime analysis. I highly recommend that software, the website has great info on how to use it (flimfit.org). But I also run the data through phasor analysis, because Leica does not export any of the phasor data in a format you can use, I calculate the phasor in Matlab.

I am currently developing a Matlab based analysis tool to be able to compare experimental data against control samples using the phasor data. I have used Cellpose to identify cells which helps with visualizing the lifetime based on different regions of interest in the image (https://imgur.com/gallery/omG9wGI). It is about 90% done so if you would like to do some beta testing, I would appreciate the feedback.

Lastly, if you are interested, I have also recorded a webinar on FLIM (https://youtu.be/Sjc4H4dTCYs).
All the best,
Deb

Deborah Barkauskas
Senior Microscopist, ACRF: Cancer Biology Imaging Facility

Institute for Molecular Bioscience
The University of Queensland
Brisbane Qld 4072 Australia
E [hidden email]
W imb.uq.edu.au/microscopy

-----Original Message-----
From: Confocal Microscopy List <[hidden email]> On Behalf Of Stanislav Vitha
Sent: Friday, 4 September 2020 2:50 AM
To: [hidden email]
Subject: Re: FLIM raw data from SP8 Falcon?

*****
To join, leave or search the confocal microscopy listserv, go to:
http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy
Post images on http://www.imgur.com and include the link in your posting.
*****

Hi Petro,
when you are in the FALCON program window (not the regular SP8 imaging panel) or just run the FALCON module offline ("LAS_X_SingleMoleculeDetection.exe" in the BIN  folder of LASX installation), go to File - Export Raw Data.
There you have the option to export as PicoQuant .ptu, Picoquant .pt3  or Picoquant FLIM binary files, .bin)


I would be interested to hear what software the general non-physicist public uses for off-line analysis of the FALCON FLIM data besides the Leica software. I started looking at FlimFit  and SimFCS, but do not quite know what I am doing yet.
I would like to be able to list an affordable option for our core facility users who do not have a Leica LASX license.

Stan

Stanislav Vitha
Microscopy and Imaging Center
Texas A&M University

[Petro]

*****
To join, leave or search the confocal microscopy listserv, go to:
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Post images on http://www.imgur.com and include the link in your posting.
*****

Hi Stan and Deb.
I second that some batch processing converted would be very useful...
Best.
Petro.

On Fri, Sep 4, 2020 at 9:10 AM Deborah Barkauskas <[hidden email]>
wrote:

> *****
> To join, leave or search the confocal microscopy listserv, go to:
> http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy
> Post images on http://www.imgur.com and include the link in your posting.
> *****
>
> Hi Petro and Stan,
>
> This is such a timely post because I just emailed my local Leica
> specialist a similar question about the .lif format so I can extract the
> raw data from the .lif file. I currently export each image by hand in the
> Leica FLIM software as described by Stan. This in itself can take hours
> depending on the imaging. I am looking for a better way to extract the data
> I need for analysis.
>
> I then run that data through FLIMFit for lifetime analysis. I highly
> recommend that software, the website has great info on how to use it (
> flimfit.org). But I also run the data through phasor analysis, because
> Leica does not export any of the phasor data in a format you can use, I
> calculate the phasor in Matlab.
>
> I am currently developing a Matlab based analysis tool to be able to
> compare experimental data against control samples using the phasor data. I
> have used Cellpose to identify cells which helps with visualizing the
> lifetime based on different regions of interest in the image (
> https://imgur.com/gallery/omG9wGI). It is about 90% done so if you would
> like to do some beta testing, I would appreciate the feedback.
>
> Lastly, if you are interested, I have also recorded a webinar on FLIM (
> https://youtu.be/Sjc4H4dTCYs).
> All the best,
> Deb
>
> Deborah Barkauskas
> Senior Microscopist, ACRF: Cancer Biology Imaging Facility
>
> Institute for Molecular Bioscience
> The University of Queensland
> Brisbane Qld 4072 Australia
> E [hidden email]
> W imb.uq.edu.au/microscopy
>
> -----Original Message-----
> From: Confocal Microscopy List <[hidden email]> On
> Behalf Of Stanislav Vitha
> Sent: Friday, 4 September 2020 2:50 AM
> To: [hidden email]
> Subject: Re: FLIM raw data from SP8 Falcon?
>
> *****
> To join, leave or search the confocal microscopy listserv, go to:
> http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy
> Post images on http://www.imgur.com and include the link in your posting.
> *****
>
> Hi Petro,
> when you are in the FALCON program window (not the regular SP8 imaging
> panel) or just run the FALCON module offline
> ("LAS_X_SingleMoleculeDetection.exe" in the BIN  folder of LASX
> installation), go to File - Export Raw Data.
> There you have the option to export as PicoQuant .ptu, Picoquant .pt3  or
> Picoquant FLIM binary files, .bin)
>
>
> I would be interested to hear what software the general non-physicist
> public uses for off-line analysis of the FALCON FLIM data besides the Leica
> software. I started looking at FlimFit  and SimFCS, but do not quite know
> what I am doing yet.
> I would like to be able to list an affordable option for our core facility
> users who do not have a Leica LASX license.
>
> Stan
>
> Stanislav Vitha
> Microscopy and Imaging Center
> Texas A&M University
>

--
______________________________
Petro Khoroshyy