extracting acquistion times from time series

[felipe-andres]

Hi,

I have a time series in the form of a big stack of tiffs (thousands of tiffs) and I'd like to extract each frame's acquisition time quickly and efficiently. I'd then like to export all of the acquisition times to a text file or an excel spreadsheet.

Any help would be hugely appreciated!

Thanks,

Felipe

[lechristophe]

Le jeudi 8 décembre 2011 à 22:53, Felipe-Andres Piedra a écrit :

> Hi,
>  
> I have a time series in the form of a big stack of tiffs (thousands of tiffs) and I'd like to extract each frame's acquisition time quickly and efficiently. I'd then like to export all of the acquisition times to a text file or an excel spreadsheet.  
>  
> Any help would be hugely appreciated!
>  
> Thanks,
>  
> Felipe

I'd also be very interested in that. I guess this is more a BioFormats question than an ImageJ one, as it deals with timestamp metadata associated with microscope file formats (that's why I CCed Curtis Rueden). Is it possible to have arbitrary time stamps or is there only a constant time interval when importing a file as an xyt stack? I seem to remember that ImageJ only allows a constant interval in this case, so the intervals are averaged if they are not strictly constant. But does it keep the real timestamp somewhere in the image metadata ?

A word on why I ask this question: when acquiring a stream of images as fast as possible (such as when doing fluorescence recovery after bleaching measurements on fast-diffusing molecules), the interval between frame can vary quite a bit. Then, knowing the precise interval would be interesting for precise fitting of the recovery curves.

Christophe

[Janne Hyötylä]

Hello Christophe and Felipe,

I wrote a macro for a similar purpose. BioFormats can read
the time stamps with arbitrary intervals. The timings are copied per
channel into the clipboard from where you can paste them into a
spreadsheet or whatever. Of course you can modify the macro to directly
write to a file.

The macro uses the getPlaneTimingDeltaT macro command from BioFormats, so
if that doesn't return anything the macro fails as well. I tested it with
plain TIFF stacks and it doesn't seem to work there. But for example for
Leica LIF files it works perfectly.
It works on one file at a time so also not sure if it would help you,
Felipe (if you indeed have thousands of separate tiff files).

I don't know how to attach files here and pasting it into the email might
mess with the formatting, so please contact me off list if you're
interested and I'll send it to you.


Cheers,
Janne


On Fri, 09 Dec 2011 00:26:26 +0100, Christophe Leterrier
<[hidden email]> wrote:

> Le jeudi 8 décembre 2011 à 22:53, Felipe-Andres Piedra a écrit :
>
>> Hi,
>>
>> I have a time series in the form of a big stack of tiffs (thousands of  
>> tiffs) and I'd like to extract each frame's acquisition time quickly  
>> and efficiently. I'd then like to export all of the acquisition times  
>> to a text file or an excel spreadsheet.
>>
>> Any help would be hugely appreciated!
>>
>> Thanks,
>>
>> Felipe
>
> I'd also be very interested in that. I guess this is more a BioFormats  
> question than an ImageJ one, as it deals with timestamp metadata  
> associated with microscope file formats (that's why I CCed Curtis  
> Rueden). Is it possible to have arbitrary time stamps or is there only a  
> constant time interval when importing a file as an xyt stack? I seem to  
> remember that ImageJ only allows a constant interval in this case, so  
> the intervals are averaged if they are not strictly constant. But does  
> it keep the real timestamp somewhere in the image metadata ?
>
> A word on why I ask this question: when acquiring a stream of images as  
> fast as possible (such as when doing fluorescence recovery after  
> bleaching measurements on fast-diffusing molecules), the interval  
> between frame can vary quite a bit. Then, knowing the precise interval  
> would be interesting for precise fitting of the recovery curves.
>
> Christophe

[ctrueden]

Hi Felipe and everyone,

I have a time series in the form of a big stack of tiffs (thousands of
> tiffs) and I'd like to extract each frame's acquisition time quickly and
> efficiently.
>

I know it's been awhile since this thread, but I wanted to clarify that
Bio-Formats does support parsing of variable time stamps, converted from
any supported format. And as Janne suggests, there are some examples that
demonstrate how to do it.

For an ImageJ macro, see planeTimings.txt, linked from:
  http://loci.wisc.edu/bio-formats/imagej

For Java code, see PrintTimestamps.java, linked from:
  http://loci.wisc.edu/bio-formats/bio-formats-java-library

HTH,
Curtis


2011/12/9 Janne Hyötylä <[hidden email]>

> Hello Christophe and Felipe,
>
> I wrote a macro for a similar purpose. BioFormats can read
> the time stamps with arbitrary intervals. The timings are copied per
> channel into the clipboard from where you can paste them into a
> spreadsheet or whatever. Of course you can modify the macro to directly
> write to a file.
>
> The macro uses the getPlaneTimingDeltaT macro command from BioFormats, so
> if that doesn't return anything the macro fails as well. I tested it with
> plain TIFF stacks and it doesn't seem to work there. But for example for
> Leica LIF files it works perfectly.
> It works on one file at a time so also not sure if it would help you,
> Felipe (if you indeed have thousands of separate tiff files).
>
> I don't know how to attach files here and pasting it into the email might
> mess with the formatting, so please contact me off list if you're
> interested and I'll send it to you.
>
>
> Cheers,
> Janne
>
>
>
> On Fri, 09 Dec 2011 00:26:26 +0100, Christophe Leterrier
> <christophe.leterrier@gmail.**com <[hidden email]>> wrote:
>
>  Le jeudi 8 décembre 2011 à 22:53, Felipe-Andres Piedra a écrit :
>>
>>  Hi,
>>>
>>> I have a time series in the form of a big stack of tiffs (thousands of
>>> tiffs) and I'd like to extract each frame's acquisition time quickly and
>>> efficiently. I'd then like to export all of the acquisition times to a text
>>> file or an excel spreadsheet.
>>>
>>> Any help would be hugely appreciated!
>>>
>>> Thanks,
>>>
>>> Felipe
>>>
>>
>> I'd also be very interested in that. I guess this is more a BioFormats
>> question than an ImageJ one, as it deals with timestamp metadata associated
>> with microscope file formats (that's why I CCed Curtis Rueden). Is it
>> possible to have arbitrary time stamps or is there only a constant time
>> interval when importing a file as an xyt stack? I seem to remember that
>> ImageJ only allows a constant interval in this case, so the intervals are
>> averaged if they are not strictly constant. But does it keep the real
>> timestamp somewhere in the image metadata ?
>>
>> A word on why I ask this question: when acquiring a stream of images as
>> fast as possible (such as when doing fluorescence recovery after bleaching
>> measurements on fast-diffusing molecules), the interval between frame can
>> vary quite a bit. Then, knowing the precise interval would be interesting
>> for precise fitting of the recovery curves.
>>
>> Christophe
>>
>