[ome-users] How to get timestamp when using bfconvert

[Curtis Rueden]

Hi Fangfei,

> So my question is that the actual time the image was taken is still
> conserved when I use bfconvert to convert nd2 to tiff, and how can I
> get that information (actual time)?

Did you have a look at this code example?
https://github.com/openmicroscopy/bioformats/blob/v5.0.6/components/formats-gpl/utils/PrintTimestamps.java

>From the output of that, you could cobble together a shell script to rename
the file(s) to include the information, if that is what you need.

Regards,
Curtis

On Tue, Dec 16, 2014 at 1:59 PM, FangfeiLi <lifangfei at hotmail.com> wrote:
>
> Hi, Moore,
>
> I think you got my idea.
> I mean when you take the photo using the microscopy, you got a nd2 file.
> The nd2 file should record the actual time each image was taken.
> The nd2 file is a video consists of all images. Therefore, each image in
> the nd2 file should contain the information of the
> actual time that the image is taken. when I use bfconvert to convert the
> nd2 file to tiff file, I want to save that information also.
>
> Using %A may give me the actual time the first image was taken in the nd2
> file. However, it could not give the actual time all
> the other images was taken in the same nd2 file. Due to there might be
> something wrong that the image was not taken as the the time I set. So I
> need to get the information of the actual time the image was taken.
>
> So my question is that the *actual time* the image was taken is still
> conserved when I use bfconvert to convert nd2 to tiff, and how can I get
> that information (*actual time*)?
>
> Thank you so much and best regards!
> Fangfei
>
> On Dec 16, 2014, at 11:19 AM, Melissa Linkert <melissa at glencoesoftware.com>
> wrote:
>
> Hi Fangfei,
>
> When I use bfconvert to convert a nd2 file into a number of tiff files,
> is there a way to extract the timestamp of each image, i.e., the time
> each image is taken by microscope camera?
>
>
> It seems like Fangfei wanted to know the timestamp of each tiff,
> E.g. timepoint 0 is 0 seconds
> timepoint 1 is 10.5 seconds
>
>
> If you are indeed hoping to record the timestamp, the only way to do so
> now is by using the %A option in the output file name, for example:
>
>  bfconvert file.nd2 output-file_%A.tiff
>
> %A gives the full timestamp of the first image stored in the output
> file.  So if the start of the acquisition was 2014-12-16T10:15:00 and
> the first image was acquired 5 seconds later, the output file name would
> be output-file_2014-12-16T10:15:05.tiff.  There is not currently a
> built-in way of recording just the timestamp from the beginning of the
> acquisition, but it could be added if that would be useful.
>
> Regards,
> -Melissa
>
> On Tue, Dec 16, 2014 at 12:11:23PM +0000, William Moore wrote:
>
> It seems like Fangfei wanted to know the timestamp of each tiff,
> E.g. timepoint 0 is 0 seconds
> timepoint 1 is 10.5 seconds
>  etc.
>
> Am I right?
>
> On 16 Dec 2014, at 11:48, "Balaji Ramalingam (Staff)" <
> b.ramalingam at dundee.ac.uk> wrote:
>
> Hi,
>
> If the question is about converting each time point into an image,
> The following example should help,
>
> bfconvert -timepoint 0 /path/to/input output-first-timepoint.tiff
>
>
> The above example converts the first time point alone (-timepoint 0).
>
> For more information on bfconvert, please follow the following link,
> http://www.openmicroscopy.org/site/support/bio-formats5/users/comlinetools/
> conversion.html
>
> Hope that helps.
>
> Best,
> Balaji
>
> __________________
> Mr Balaji Ramalingam
> Software Developer
>
> OME Team
> College of Life Sciences
> University of Dundee
>
>
>
>
>
>
> On 15/12/2014 18:59, "FangfeiLi" <lifangfei at hotmail.com> wrote:
>
> Hello,
>
> May I ask a question?
>
> When I use bfconvert to convert a nd2 file into a number of tiff files,
> is there a way to extract the timestamp of each image, i.e., the time
> each image is taken by microscope camera?
>
> Thank you very much and best regards!
> Fangfei
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