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<p dir="ltr">Hi,</p>
<p dir="ltr">I'm interested, too.<br>
a2</p>
<div class="gmail_quote">On Dec 17, 2014 1:00 PM, ome-users-request@lists.openmicroscopy.org.uk wrote:<br type="attribution">
<blockquote class="quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
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Today's Topics:<br>
<br>
1. Re: How to get timestamp when using bfconvert (William Moore)<br>
2. Huygens H5 (Philippe Mailly)<br>
3. Re: Huygens H5 (Mark Carroll)<br>
4. Re: Huygens H5 (Niko Ehrenfeuchter)<br>
5. Groups visibility (Philippe Mailly)<br>
6. Re: Groups visibility (William Moore)<br>
7. Re: How to get timestamp when using bfconvert (Melissa Linkert)<br>
8. Re: How to get timestamp when using bfconvert (FangfeiLi)<br>
9. Re: How to get timestamp when using bfconvert (Curtis Rueden)<br>
<br>
<br>
----------------------------------------------------------------------<br>
<br>
Message: 1<br>
Date: Tue, 16 Dec 2014 12:11:23 +0000<br>
From: William Moore <will@lifesci.dundee.ac.uk><br>
To: "Balaji Ramalingam (Staff)" <b.ramalingam@dundee.ac.uk><br>
Cc: FangfeiLi <lifangfei@hotmail.com>,<br>
"ome-users@lists.openmicroscopy.org.uk"<br>
<ome-users@lists.openmicroscopy.org.uk><br>
Subject: Re: [ome-users] How to get timestamp when using bfconvert<br>
Message-ID:<br>
<84FB2A13-046F-4E3E-AAF8-38C76E647921@lifesci.dundee.ac.uk><br>
Content-Type: text/plain; charset=us-ascii<br>
<br>
It seems like Fangfei wanted to know the timestamp of each tiff,<br>
E.g. timepoint 0 is 0 seconds<br>
timepoint 1 is 10.5 seconds<br>
etc.<br>
<br>
Am I right?<br>
<br>
On 16 Dec 2014, at 11:48, "Balaji Ramalingam (Staff)" <b.ramalingam@dundee.ac.uk> wrote:<br>
<br>
> Hi,<br>
> <br>
> If the question is about converting each time point into an image,<br>
> The following example should help,<br>
> <br>
> bfconvert -timepoint 0 /path/to/input output-first-timepoint.tiff<br>
> <br>
> <br>
> The above example converts the first time point alone (-timepoint 0).<br>
> <br>
> For more information on bfconvert, please follow the following link,<br>
> <a href="http://www.openmicroscopy.org/site/support/bio-formats5/users/comlinetools/">
http://www.openmicroscopy.org/site/support/bio-formats5/users/comlinetools/</a><br>
> conversion.html<br>
> <br>
> Hope that helps.<br>
> <br>
> Best,<br>
> Balaji<br>
> <br>
> __________________<br>
> Mr Balaji Ramalingam<br>
> Software Developer<br>
> <br>
> OME Team<br>
> College of Life Sciences<br>
> University of Dundee<br>
> <br>
> <br>
> <br>
> <br>
> <br>
> <br>
> On 15/12/2014 18:59, "FangfeiLi" <lifangfei@hotmail.com> wrote:<br>
> <br>
>> Hello,<br>
>> <br>
>> May I ask a question?<br>
>> <br>
>> When I use bfconvert to convert a nd2 file into a number of tiff files,<br>
>> is there a way to extract the timestamp of each image, i.e., the time<br>
>> each image is taken by microscope camera?<br>
>> <br>
>> Thank you very much and best regards!<br>
>> Fangfei<br>
>> _______________________________________________<br>
>> ome-users mailing list<br>
>> ome-users@lists.openmicroscopy.org.uk<br>
>> <a href="http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-users">http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-users</a><br>
> <br>
> <br>
> The University of Dundee is a registered Scottish Charity, No: SC015096<br>
> _______________________________________________<br>
> ome-users mailing list<br>
> ome-users@lists.openmicroscopy.org.uk<br>
> <a href="http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-users">http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-users</a><br>
<br>
<br>
<br>
------------------------------<br>
<br>
Message: 2<br>
Date: Tue, 16 Dec 2014 15:00:01 +0100<br>
From: Philippe Mailly <philippe.mailly@college-de-france.fr><br>
To: ome-users@lists.openmicroscopy.org.uk<br>
Subject: [ome-users] Huygens H5<br>
Message-ID: <54903AE1.5060804@college-de-france.fr><br>
Content-Type: text/plain; charset="utf-8"; Format="flowed"<br>
<br>
Hi,<br>
<br>
Is it a LOCI roadmap to read huygens h5 file format ??<br>
<br>
<br>
Philippe<br>
<br>
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Message: 3<br>
Date: Tue, 16 Dec 2014 14:04:00 +0000<br>
From: Mark Carroll <m.t.b.carroll@dundee.ac.uk><br>
To: <ome-users@lists.openmicroscopy.org.uk><br>
Subject: Re: [ome-users] Huygens H5<br>
Message-ID: <54903BD0.2050000@dundee.ac.uk><br>
Content-Type: text/plain; charset="windows-1252"; format=flowed<br>
<br>
Dear Philippe,<br>
<br>
> Is it a LOCI roadmap to read huygens h5 file format ??<br>
<br>
We do have a relevant ticket noted at<br>
<a href="http://trac.openmicroscopy.org/ome/ticket/4104">http://trac.openmicroscopy.org/ome/ticket/4104</a> and would be glad to add<br>
you, or anybody else interested, to the cc: list so that you receive<br>
updates.<br>
<br>
-- Mark<br>
<br>
The University of Dundee is a registered Scottish Charity, No: SC015096<br>
<br>
<br>
------------------------------<br>
<br>
Message: 4<br>
Date: Tue, 16 Dec 2014 15:12:54 +0100<br>
From: Niko Ehrenfeuchter <nikolaus.ehrenfeuchter@unibas.ch><br>
To: ome-users@lists.openmicroscopy.org.uk<br>
Subject: Re: [ome-users] Huygens H5<br>
Message-ID: <54903DE6.5080601@unibas.ch><br>
Content-Type: text/plain; charset=ISO-8859-1; format=flowed<br>
<br>
Dear Philippe,<br>
<br>
as long as BioFormats doesn't read it, at least for Fiji you can work <br>
around it by using the HDF5 plugin provided here:<br>
<br>
<a href="http://lmb.informatik.uni-freiburg.de/resources/opensource/imagej_plugins/hdf5.html">http://lmb.informatik.uni-freiburg.de/resources/opensource/imagej_plugins/hdf5.html</a><br>
<br>
When importing SVI-HDF5 files with it, make sure to select the image <br>
dataset from the path and check the "individual hyperstacks (custom <br>
layout)" option.<br>
<br>
Then put "tczyx" into the "data set layout" field and click "load".<br>
<br>
Cheers<br>
Niko<br>
<br>
<br>
On 16.12.2014 15:04, Mark Carroll wrote:<br>
> Dear Philippe,<br>
><br>
>> Is it a LOCI roadmap to read huygens h5 file format ??<br>
><br>
> We do have a relevant ticket noted at<br>
> <a href="http://trac.openmicroscopy.org/ome/ticket/4104">http://trac.openmicroscopy.org/ome/ticket/4104</a> and would be glad to add<br>
> you, or anybody else interested, to the cc: list so that you receive<br>
> updates.<br>
><br>
> -- Mark<br>
><br>
> The University of Dundee is a registered Scottish Charity, No: SC015096<br>
> _______________________________________________<br>
> ome-users mailing list<br>
> ome-users@lists.openmicroscopy.org.uk<br>
> <a href="http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-users">http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-users</a><br>
<br>
-- <br>
Niko Ehrenfeuchter | Image Analysis Specialist | Biozentrum, University <br>
of Basel | Klingelbergstr. 50/70 | CH-4056 Basel<br>
Phone: +41 (61) 26 72673 | nikolaus.ehrenfeuchter@unibas.ch | <br>
<a href="http://www.biozentrum.unibas.ch">www.biozentrum.unibas.ch</a> | <a href="http://www.microscopynetwork.unibas.ch">
www.microscopynetwork.unibas.ch</a><br>
<br>
<br>
------------------------------<br>
<br>
Message: 5<br>
Date: Tue, 16 Dec 2014 16:47:19 +0100<br>
From: Philippe Mailly <philippe.mailly@college-de-france.fr><br>
To: ome-users@lists.openmicroscopy.org.uk<br>
Subject: [ome-users] Groups visibility<br>
Message-ID: <54905407.90706@college-de-france.fr><br>
Content-Type: text/plain; charset="utf-8"; Format="flowed"<br>
<br>
Hi,<br>
<br>
I have the rights administrator and I discovered that if I do a <br>
connexion via Insight I can see only groups that I'm the owner, but if I <br>
do a connexion via the web client I can see all groups and images ????<br>
Is it a "special" issue from the web client ?<br>
<br>
Philippe<br>
<br>
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<br>
Message: 6<br>
Date: Tue, 16 Dec 2014 15:52:07 +0000<br>
From: William Moore <will@lifesci.dundee.ac.uk><br>
To: Philippe Mailly <philippe.mailly@college-de-france.fr><br>
Cc: ome-users@lists.openmicroscopy.org.uk<br>
Subject: Re: [ome-users] Groups visibility<br>
Message-ID:<br>
<377D5F59-1F97-4DF2-9067-331F9CA6E2A0@lifesci.dundee.ac.uk><br>
Content-Type: text/plain; charset=us-ascii<br>
<br>
Hi Philippe,<br>
<br>
Yes, this feature only exists in web client at the moment.<br>
It is useful for accessing all data that you have permissions to see.<br>
I am not sure whether we are planning to add this to Insight any time soon.<br>
<br>
Will.<br>
<br>
<br>
On 16 Dec 2014, at 15:47, Philippe Mailly <philippe.mailly@college-de-france.fr> wrote:<br>
<br>
> Hi,<br>
> <br>
> I have the rights administrator and I discovered that if I do a connexion via Insight I can see only groups that I'm the owner, but if I do a connexion via the web client I can see all groups and images ????<br>
> Is it a "special" issue from the web client ?<br>
> <br>
> Philippe<br>
> <br>
> <philippe_mailly.vcf>_______________________________________________<br>
> ome-users mailing list<br>
> ome-users@lists.openmicroscopy.org.uk<br>
> <a href="http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-users">http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-users</a><br>
<br>
<br>
<br>
------------------------------<br>
<br>
Message: 7<br>
Date: Tue, 16 Dec 2014 10:19:45 -0600<br>
From: Melissa Linkert <melissa@glencoesoftware.com><br>
To: FangfeiLi <lifangfei@hotmail.com><br>
Cc: "ome-users@lists.openmicroscopy.org.uk"<br>
<ome-users@lists.openmicroscopy.org.uk><br>
Subject: Re: [ome-users] How to get timestamp when using bfconvert<br>
Message-ID: <20141216161945.GA2367@hera><br>
Content-Type: text/plain; charset=us-ascii<br>
<br>
Hi Fangfei,<br>
<br>
> >> When I use bfconvert to convert a nd2 file into a number of tiff files,<br>
> >> is there a way to extract the timestamp of each image, i.e., the time<br>
> >> each image is taken by microscope camera?<br>
<br>
> It seems like Fangfei wanted to know the timestamp of each tiff,<br>
> E.g. timepoint 0 is 0 seconds<br>
> timepoint 1 is 10.5 seconds<br>
<br>
If you are indeed hoping to record the timestamp, the only way to do so<br>
now is by using the %A option in the output file name, for example:<br>
<br>
bfconvert file.nd2 output-file_%A.tiff<br>
<br>
%A gives the full timestamp of the first image stored in the output<br>
file. So if the start of the acquisition was 2014-12-16T10:15:00 and<br>
the first image was acquired 5 seconds later, the output file name would<br>
be output-file_2014-12-16T10:15:05.tiff. There is not currently a<br>
built-in way of recording just the timestamp from the beginning of the<br>
acquisition, but it could be added if that would be useful.<br>
<br>
Regards,<br>
-Melissa<br>
<br>
On Tue, Dec 16, 2014 at 12:11:23PM +0000, William Moore wrote:<br>
> It seems like Fangfei wanted to know the timestamp of each tiff,<br>
> E.g. timepoint 0 is 0 seconds<br>
> timepoint 1 is 10.5 seconds<br>
> etc.<br>
> <br>
> Am I right?<br>
> <br>
> On 16 Dec 2014, at 11:48, "Balaji Ramalingam (Staff)" <b.ramalingam@dundee.ac.uk> wrote:<br>
> <br>
> > Hi,<br>
> > <br>
> > If the question is about converting each time point into an image,<br>
> > The following example should help,<br>
> > <br>
> > bfconvert -timepoint 0 /path/to/input output-first-timepoint.tiff<br>
> > <br>
> > <br>
> > The above example converts the first time point alone (-timepoint 0).<br>
> > <br>
> > For more information on bfconvert, please follow the following link,<br>
> > <a href="http://www.openmicroscopy.org/site/support/bio-formats5/users/comlinetools/">
http://www.openmicroscopy.org/site/support/bio-formats5/users/comlinetools/</a><br>
> > conversion.html<br>
> > <br>
> > Hope that helps.<br>
> > <br>
> > Best,<br>
> > Balaji<br>
> > <br>
> > __________________<br>
> > Mr Balaji Ramalingam<br>
> > Software Developer<br>
> > <br>
> > OME Team<br>
> > College of Life Sciences<br>
> > University of Dundee<br>
> > <br>
> > <br>
> > <br>
> > <br>
> > <br>
> > <br>
> > On 15/12/2014 18:59, "FangfeiLi" <lifangfei@hotmail.com> wrote:<br>
> > <br>
> >> Hello,<br>
> >> <br>
> >> May I ask a question?<br>
> >> <br>
> >> When I use bfconvert to convert a nd2 file into a number of tiff files,<br>
> >> is there a way to extract the timestamp of each image, i.e., the time<br>
> >> each image is taken by microscope camera?<br>
> >> <br>
> >> Thank you very much and best regards!<br>
> >> Fangfei<br>
> >> _______________________________________________<br>
> >> ome-users mailing list<br>
> >> ome-users@lists.openmicroscopy.org.uk<br>
> >> <a href="http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-users">http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-users</a><br>
> > <br>
> > <br>
> > The University of Dundee is a registered Scottish Charity, No: SC015096<br>
> > _______________________________________________<br>
> > ome-users mailing list<br>
> > ome-users@lists.openmicroscopy.org.uk<br>
> > <a href="http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-users">http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-users</a><br>
> <br>
> _______________________________________________<br>
> ome-users mailing list<br>
> ome-users@lists.openmicroscopy.org.uk<br>
> <a href="http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-users">http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-users</a><br>
<br>
<br>
------------------------------<br>
<br>
Message: 8<br>
Date: Tue, 16 Dec 2014 14:59:40 -0500<br>
From: FangfeiLi <lifangfei@hotmail.com><br>
To: melissa@glencoesoftware.com<br>
Cc: "ome-users@lists.openmicroscopy.org.uk"<br>
<ome-users@lists.openmicroscopy.org.uk><br>
Subject: Re: [ome-users] How to get timestamp when using bfconvert<br>
Message-ID: <BLU436-SMTP514C1BBE2BDE67A97F94DDAE6C0@phx.gbl><br>
Content-Type: text/plain; charset="us-ascii"<br>
<br>
Hi, Moore,<br>
<br>
I think you got my idea.<br>
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.<br>
The nd2 file is a video consists of all images. Therefore, each image in the nd2 file should contain the information of the
<br>
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.<br>
<br>
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
<br>
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.
<br>
<br>
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)?<br>
<br>
Thank you so much and best regards!<br>
Fangfei<br>
<br>
> On Dec 16, 2014, at 11:19 AM, Melissa Linkert <melissa@glencoesoftware.com> wrote:<br>
> <br>
> Hi Fangfei,<br>
> <br>
>>>> When I use bfconvert to convert a nd2 file into a number of tiff files,<br>
>>>> is there a way to extract the timestamp of each image, i.e., the time<br>
>>>> each image is taken by microscope camera?<br>
> <br>
>> It seems like Fangfei wanted to know the timestamp of each tiff,<br>
>> E.g. timepoint 0 is 0 seconds<br>
>> timepoint 1 is 10.5 seconds<br>
> <br>
> If you are indeed hoping to record the timestamp, the only way to do so<br>
> now is by using the %A option in the output file name, for example:<br>
> <br>
> bfconvert file.nd2 output-file_%A.tiff<br>
> <br>
> %A gives the full timestamp of the first image stored in the output<br>
> file. So if the start of the acquisition was 2014-12-16T10:15:00 and<br>
> the first image was acquired 5 seconds later, the output file name would<br>
> be output-file_2014-12-16T10:15:05.tiff. There is not currently a<br>
> built-in way of recording just the timestamp from the beginning of the<br>
> acquisition, but it could be added if that would be useful.<br>
> <br>
> Regards,<br>
> -Melissa<br>
> <br>
> On Tue, Dec 16, 2014 at 12:11:23PM +0000, William Moore wrote:<br>
>> It seems like Fangfei wanted to know the timestamp of each tiff,<br>
>> E.g. timepoint 0 is 0 seconds<br>
>> timepoint 1 is 10.5 seconds<br>
>> etc.<br>
>> <br>
>> Am I right?<br>
>> <br>
>> On 16 Dec 2014, at 11:48, "Balaji Ramalingam (Staff)" <b.ramalingam@dundee.ac.uk> wrote:<br>
>> <br>
>>> Hi,<br>
>>> <br>
>>> If the question is about converting each time point into an image,<br>
>>> The following example should help,<br>
>>> <br>
>>> bfconvert -timepoint 0 /path/to/input output-first-timepoint.tiff<br>
>>> <br>
>>> <br>
>>> The above example converts the first time point alone (-timepoint 0).<br>
>>> <br>
>>> For more information on bfconvert, please follow the following link,<br>
>>> <a href="http://www.openmicroscopy.org/site/support/bio-formats5/users/comlinetools/">
http://www.openmicroscopy.org/site/support/bio-formats5/users/comlinetools/</a><br>
>>> conversion.html<br>
>>> <br>
>>> Hope that helps.<br>
>>> <br>
>>> Best,<br>
>>> Balaji<br>
>>> <br>
>>> __________________<br>
>>> Mr Balaji Ramalingam<br>
>>> Software Developer<br>
>>> <br>
>>> OME Team<br>
>>> College of Life Sciences<br>
>>> University of Dundee<br>
>>> <br>
>>> <br>
>>> <br>
>>> <br>
>>> <br>
>>> <br>
>>> On 15/12/2014 18:59, "FangfeiLi" <lifangfei@hotmail.com> wrote:<br>
>>> <br>
>>>> Hello,<br>
>>>> <br>
>>>> May I ask a question?<br>
>>>> <br>
>>>> When I use bfconvert to convert a nd2 file into a number of tiff files,<br>
>>>> is there a way to extract the timestamp of each image, i.e., the time<br>
>>>> each image is taken by microscope camera?<br>
>>>> <br>
>>>> Thank you very much and best regards!<br>
>>>> Fangfei<br>
>>>> _______________________________________________<br>
>>>> ome-users mailing list<br>
>>>> ome-users@lists.openmicroscopy.org.uk<br>
>>>> <a href="http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-users">http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-users</a><br>
>>> <br>
>>> <br>
>>> The University of Dundee is a registered Scottish Charity, No: SC015096<br>
>>> _______________________________________________<br>
>>> ome-users mailing list<br>
>>> ome-users@lists.openmicroscopy.org.uk<br>
>>> <a href="http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-users">http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-users</a><br>
>> <br>
>> _______________________________________________<br>
>> ome-users mailing list<br>
>> ome-users@lists.openmicroscopy.org.uk<br>
>> <a href="http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-users">http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-users</a><br>
<br>
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<br>
Message: 9<br>
Date: Tue, 16 Dec 2014 14:04:30 -0600<br>
From: Curtis Rueden <ctrueden@wisc.edu><br>
To: FangfeiLi <lifangfei@hotmail.com><br>
Cc: "ome-users@lists.openmicroscopy.org.uk"<br>
<ome-users@lists.openmicroscopy.org.uk><br>
Subject: Re: [ome-users] How to get timestamp when using bfconvert<br>
Message-ID:<br>
<CADN69ymQvk+sQP-_KhTRibUDUmEsukjNfRTykMWdthy-qb0e8Q@mail.gmail.com><br>
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<br>
Hi Fangfei,<br>
<br>
> So my question is that the actual time the image was taken is still<br>
> conserved when I use bfconvert to convert nd2 to tiff, and how can I<br>
> get that information (actual time)?<br>
<br>
Did you have a look at this code example?<br>
<a href="https://github.com/openmicroscopy/bioformats/blob/v5.0.6/components/formats-gpl/utils/PrintTimestamps.java">https://github.com/openmicroscopy/bioformats/blob/v5.0.6/components/formats-gpl/utils/PrintTimestamps.java</a><br>
<br>
>From the output of that, you could cobble together a shell script to rename<br>
the file(s) to include the information, if that is what you need.<br>
<br>
Regards,<br>
Curtis<br>
<br>
On Tue, Dec 16, 2014 at 1:59 PM, FangfeiLi <lifangfei@hotmail.com> wrote:<br>
><br>
> Hi, Moore,<br>
><br>
> I think you got my idea.<br>
> I mean when you take the photo using the microscopy, you got a nd2 file.<br>
> The nd2 file should record the actual time each image was taken.<br>
> The nd2 file is a video consists of all images. Therefore, each image in<br>
> the nd2 file should contain the information of the<br>
> actual time that the image is taken. when I use bfconvert to convert the<br>
> nd2 file to tiff file, I want to save that information also.<br>
><br>
> Using %A may give me the actual time the first image was taken in the nd2<br>
> file. However, it could not give the actual time all<br>
> the other images was taken in the same nd2 file. Due to there might be<br>
> something wrong that the image was not taken as the the time I set. So I<br>
> need to get the information of the actual time the image was taken.<br>
><br>
> So my question is that the *actual time* the image was taken is still<br>
> conserved when I use bfconvert to convert nd2 to tiff, and how can I get<br>
> that information (*actual time*)?<br>
><br>
> Thank you so much and best regards!<br>
> Fangfei<br>
><br>
> On Dec 16, 2014, at 11:19 AM, Melissa Linkert <melissa@glencoesoftware.com><br>
> wrote:<br>
><br>
> Hi Fangfei,<br>
><br>
> When I use bfconvert to convert a nd2 file into a number of tiff files,<br>
> is there a way to extract the timestamp of each image, i.e., the time<br>
> each image is taken by microscope camera?<br>
><br>
><br>
> It seems like Fangfei wanted to know the timestamp of each tiff,<br>
> E.g. timepoint 0 is 0 seconds<br>
> timepoint 1 is 10.5 seconds<br>
><br>
><br>
> If you are indeed hoping to record the timestamp, the only way to do so<br>
> now is by using the %A option in the output file name, for example:<br>
><br>
> bfconvert file.nd2 output-file_%A.tiff<br>
><br>
> %A gives the full timestamp of the first image stored in the output<br>
> file. So if the start of the acquisition was 2014-12-16T10:15:00 and<br>
> the first image was acquired 5 seconds later, the output file name would<br>
> be output-file_2014-12-16T10:15:05.tiff. There is not currently a<br>
> built-in way of recording just the timestamp from the beginning of the<br>
> acquisition, but it could be added if that would be useful.<br>
><br>
> Regards,<br>
> -Melissa<br>
><br>
> On Tue, Dec 16, 2014 at 12:11:23PM +0000, William Moore wrote:<br>
><br>
> It seems like Fangfei wanted to know the timestamp of each tiff,<br>
> E.g. timepoint 0 is 0 seconds<br>
> timepoint 1 is 10.5 seconds<br>
> etc.<br>
><br>
> Am I right?<br>
><br>
> On 16 Dec 2014, at 11:48, "Balaji Ramalingam (Staff)" <<br>
> b.ramalingam@dundee.ac.uk> wrote:<br>
><br>
> Hi,<br>
><br>
> If the question is about converting each time point into an image,<br>
> The following example should help,<br>
><br>
> bfconvert -timepoint 0 /path/to/input output-first-timepoint.tiff<br>
><br>
><br>
> The above example converts the first time point alone (-timepoint 0).<br>
><br>
> For more information on bfconvert, please follow the following link,<br>
> <a href="http://www.openmicroscopy.org/site/support/bio-formats5/users/comlinetools/">
http://www.openmicroscopy.org/site/support/bio-formats5/users/comlinetools/</a><br>
> conversion.html<br>
><br>
> Hope that helps.<br>
><br>
> Best,<br>
> Balaji<br>
><br>
> __________________<br>
> Mr Balaji Ramalingam<br>
> Software Developer<br>
><br>
> OME Team<br>
> College of Life Sciences<br>
> University of Dundee<br>
><br>
><br>
><br>
><br>
><br>
><br>
> On 15/12/2014 18:59, "FangfeiLi" <lifangfei@hotmail.com> wrote:<br>
><br>
> Hello,<br>
><br>
> May I ask a question?<br>
><br>
> When I use bfconvert to convert a nd2 file into a number of tiff files,<br>
> is there a way to extract the timestamp of each image, i.e., the time<br>
> each image is taken by microscope camera?<br>
><br>
> Thank you very much and best regards!<br>
> Fangfei<br>
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