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Unable to open .pt3 files (Mac and Windows) #89

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phubert52 opened this Issue Jan 13, 2015 · 15 comments

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@phubert52

phubert52 commented Jan 13, 2015

PyCorrFit 0.8.5 won't open .pt3 files (both in Mac OsX 10.8.6 and Windows 7).

image

Is there some pretreatment needed ?

Many thanks (again)
Pierre

@paulmueller

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paulmueller commented Jan 13, 2015

Hi Pierre,
could you upload the file somewhere so I can have a look at what really happens?
Cheers,
Paul

@phubert52

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phubert52 commented Jan 13, 2015

Hi Paul,

here are two files, no password. First is Atto, second some protein
in solution:


https://bfs.imm.cnrs.fr/bfs/files/a3f05c53f4109afd3d01f3e17ef49b0d/ATTO488.pt3

https://bfs.imm.cnrs.fr/bfs/files/14b35877e62570d20ec195ed89bd4d05/Point_4.pt3

We are really looking forward to be using your software. Many many
thanks

Pierre

Le 13/01/15 14:17, Paul Müller a
  écrit :


  Hi Pierre,
    could you upload the file somewhere so I can have a look at what
    really happens?
    Cheers,
    Paul
  —
    Reply to this email directly or view
      it on GitHub.









-- 


  -----------------------------------------------
  Dr. Pierre Hubert, M.D., Ph.D. 
  LISM, CNRS-AMU UMR 7255, 31 Chemin Joseph Aiguier 
  13402 Marseille cedex20    France    
  tel. +33 (0)4 91 16 44 95    fax  +33 (0)4 91 71 21 24 
  http://www.researchgate.net/profile/Pierre_Hubert/

@paulmueller paulmueller added the bug label Jan 13, 2015

@phubert52

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phubert52 commented Jan 14, 2015

Hi,
I checked the computers I used, the mac is 32 bits, the PC 64. Also I tried some sample files from PicoQuant, PyCorrFit 0.8.5 is able to open them on both machines. Such a file is here:
https://bfs.imm.cnrs.fr/bfs/files/9c12b324e07b48ff6fae0b74efeeca91/Cy5_diff_IRF_FLCS_pattern.pt3
My own .pt3 files come from a LSM upgrade kit, could that make a difference ?

Best,
Pierre

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paulmueller commented Jan 14, 2015

The issue is fixed upstream, I will have to see how easy it is to make it work with PyCorrFit.

Cheers,
Paul

@phubert52

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phubert52 commented Jan 26, 2015

Hi Paul,

May I ask what is the current situation with pt3 files and PyCorrFit
?

Many thanks,
Best
Pierre

Le 14/01/15 17:03, Paul Müller a
  écrit :


  The issue is fixed upstream, I will have to see how easy it is
    to make it work with PyCorrFit.
  Cheers,
    Paul
  —
    Reply to this email directly or view
      it on GitHub.









-- 


  -----------------------------------------------
  Dr. Pierre Hubert, M.D., Ph.D. 
  LISM, CNRS-AMU UMR 7255, 31 Chemin Joseph Aiguier 
  13402 Marseille cedex20    France    
  tel. +33 (0)4 91 16 44 95    fax  +33 (0)4 91 71 21 24 
  http://www.researchgate.net/profile/Pierre_Hubert/
@paulmueller

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paulmueller commented Jan 26, 2015

Hi Pierre,

I still need to fuse the new script files from FCS_point_correlator with the PyCorrFit readfiles module. In principle, there is nothing in my way, except a lack of time. I hope this is not a big problem for you. I will get to it as soon as I am able to, but right now I am busy with a couple of other things. Keep in mind that I am doing this in my free time, i.e. I am not (yet) getting paid for developing PyCorrFit ;).

Cheers,
Paul

@phubert52

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phubert52 commented Jan 27, 2015

Hi Paul.

Thanks for your answer. I certainly didn't mean to be pushy.

We are eager to use your software (especially a PhD student in the
lab) because we are having some problems with our current analysis
(SymphoTime 32). I am a cell biologist, and anything that can make
the use of equations more palatable is welcome.

Please keep me informed of your progress.
All the best.
Pierre

Le 26/01/15 19:44, Paul Müller a
  écrit :


  Hi Pierre,
  I still need to fuse the new script files from
    FCS_point_correlator with the PyCorrFit readfiles module. In
    principle, there is nothing in my way, except a lack of time. I
    hope this is not a big problem for you. I will get to it as soon
    as I am able to, but right now I am busy with a couple of other
    things. Keep in mind that I am doing this in my free time, i.e.
    I am not (yet) getting paid for developing PyCorrFit ;). 
  Cheers,
    Paul
  —
    Reply to this email directly or view
      it on GitHub.









-- 


  -----------------------------------------------
  Dr. Pierre Hubert, M.D., Ph.D. 
  LISM, CNRS-AMU UMR 7255, 31 Chemin Joseph Aiguier 
  13402 Marseille cedex20    France    
  tel. +33 (0)4 91 16 44 95    fax  +33 (0)4 91 71 21 24 
  http://www.researchgate.net/profile/Pierre_Hubert/
@snizzleorg

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snizzleorg commented Jan 27, 2015

@phubert52 slightly off topic: what is the problem you are facing with the SymPhoTime32? - Maybe the PicoQuant Support (http://support.picoquant.com) can help?

@phubert52

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phubert52 commented Jan 27, 2015

We want to analyse simultaneously several FCS curves, that's why we
are interested in PyCorrFit.
PH

Le 27/01/15 17:29, snizzleorg a écrit :


  @phubert52 slightly off topic: what
    is the problem you are facing with the SymPhoTime32? - Maybe the
    PicoQuant Support (http://support.picoquant.com)
    can help? 
  —
    Reply to this email directly or view
      it on GitHub.









-- 


  -----------------------------------------------
  Dr. Pierre Hubert, M.D., Ph.D. 
  LISM, CNRS-AMU UMR 7255, 31 Chemin Joseph Aiguier 
  13402 Marseille cedex20    France    
  tel. +33 (0)4 91 16 44 95    fax  +33 (0)4 91 71 21 24 
  http://www.researchgate.net/profile/Pierre_Hubert/
@snizzleorg

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snizzleorg commented Jan 27, 2015

SymPhoTime64 offers that. If you want I can ask for a Demo licence for you...

@phubert52

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phubert52 commented Jan 28, 2015

Yes, thank you. 

I know there is a version 2.0 of ST64, I have to contact the
PicoQuant representative.


Le 27/01/15 17:43, snizzleorg a écrit :


  SymPhoTime64 offers that. If you want I can ask for a Demo
    licence for you...
  —
    Reply to this email directly or view
      it on GitHub.









-- 


  -----------------------------------------------
  Dr. Pierre Hubert, M.D., Ph.D. 
  LISM, CNRS-AMU UMR 7255, 31 Chemin Joseph Aiguier 
  13402 Marseille cedex20    France    
  tel. +33 (0)4 91 16 44 95    fax  +33 (0)4 91 71 21 24 
  http://www.researchgate.net/profile/Pierre_Hubert/

paulmueller pushed a commit that referenced this issue Jan 28, 2015

@paulmueller

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paulmueller commented Jan 29, 2015

Hello,
I uploaded a new release 0.8.5-pt3dev1.
https://github.com/paulmueller/PyCorrFit/releases
Could you please check if this version can open your files correctly?
Unfortunately, the links you supplied are not valid anymore. If you have no objections, I would like to upload them to GitHub as example files. Could you re-upload the pt3-files (optionally with some background information for the wiki)?
Cheers,
Paul

@phubert52

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phubert52 commented Jan 30, 2015

Hi Paul,

many thanks for the info and your work.

I will not be in the lab until next Tuesday, but I'll try the new
version as soon as possible. And of course I'll send again some pt3
files with details. Our file server does not allow for long term file
storage.

Best
Pierre

On 29/01/15 22:20, Paul Müller wrote:

Hello,
I uploaded a new release 0.8.5-pt3dev1.
https://github.com/paulmueller/PyCorrFit/releases
Could you please check if this version can open your files correctly?
Unfortunately, the links you supplied are not valid anymore. If you
have no objections, I would like to upload them to GitHub as example
files. Could you re-upload the pt3-files (optionally with some
background information for the wiki)?
Cheers,
Paul


Reply to this email directly or view it on GitHub
#89 (comment).

Dr. Pierre Hubert, M.D., Ph.D.
LISM, CNRS UPR 9027 31 Chemin Joseph Aiguier
13402 Marseille cedex20 France
http://lism.cnrs-mrs.fr/JS_files/Page_JS
tel. +33 (0)4 91 16 44 95
fax +33 (0)4 91 71 21 24

@phubert52

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phubert52 commented Feb 6, 2015

Hi Paul,

Sorry it took me some time to come back to you.

And many thanks for your work. PyCorrFit opens now our .pt3 files
without problem.

I am putting a zip containing 6 such files in our file server :
https://bfs.imm.cnrs.fr/bfs/files/e30fd2bd3b08f7f158094e3d91932fe1/A42F_4jul2014.zip
;
no password, files will be there for 7 days

Data are single channel acquisitions of a monomeric membrane protein
(~ 30kDa) in detergent (DDM) solution, labeled with atto 488.
Equipment was a PicoQuant LSM upgrade on an Olympus FV1000
microscope, with SymphoTime32; PQ pulsed laser 470 nm, 60x oil
objective, PQ SPAD detector. Is that sufficient info ?

Would mind mentioning the name of Ms. Victoria Schmidt, PhD student,
who prepared the protein and ran the FCS with me ?

Many thanks again, I'll keep you informed of our progresses with
your software.

Best
Pierre

Le 29/01/15 22:20, Paul Müller a
  écrit :


  Hello,
    I uploaded a new release 0.8.5-pt3dev1. 
    https://github.com/paulmueller/PyCorrFit/releases
    Could you please check if this version can open your files
    correctly?
    Unfortunately, the links you supplied are not valid anymore. If
    you have no objections, I would like to upload them to GitHub as
    example files. Could you re-upload the pt3-files (optionally
    with some background information for the wiki)?
    Cheers,
    Paul
  —
    Reply to this email directly or view
      it on GitHub.
@paulmueller

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paulmueller commented Feb 6, 2015

Great!

for your reference, I added an Examples section to the wiki. You should be able to change it if you want to add anything.

Best,
Paul

@paulmueller paulmueller closed this Feb 6, 2015

@paulmueller paulmueller referenced this issue Feb 6, 2015

Merged

Pt3 dev #91

paulmueller pushed a commit that referenced this issue Sep 30, 2015

paulmueller
Had 30mins for issue #89. It seems like the pt3 file import works. St…
…ay tuned for an alpha binary.

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