[ome-users] Huygens H5
Ponti Aaron
aaron.ponti at bsse.ethz.ch
Wed Dec 17 12:21:46 GMT 2014
Hi,
I'm interested, too.
a2
On Dec 17, 2014 1:00 PM, ome-users-request at lists.openmicroscopy.org.uk wrote:
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Today's Topics:
1. Re: How to get timestamp when using bfconvert (William Moore)
2. Huygens H5 (Philippe Mailly)
3. Re: Huygens H5 (Mark Carroll)
4. Re: Huygens H5 (Niko Ehrenfeuchter)
5. Groups visibility (Philippe Mailly)
6. Re: Groups visibility (William Moore)
7. Re: How to get timestamp when using bfconvert (Melissa Linkert)
8. Re: How to get timestamp when using bfconvert (FangfeiLi)
9. Re: How to get timestamp when using bfconvert (Curtis Rueden)
----------------------------------------------------------------------
Message: 1
Date: Tue, 16 Dec 2014 12:11:23 +0000
From: William Moore <will at lifesci.dundee.ac.uk>
To: "Balaji Ramalingam (Staff)" <b.ramalingam at dundee.ac.uk>
Cc: FangfeiLi <lifangfei at hotmail.com>,
"ome-users at lists.openmicroscopy.org.uk"
<ome-users at lists.openmicroscopy.org.uk>
Subject: Re: [ome-users] How to get timestamp when using bfconvert
Message-ID:
<84FB2A13-046F-4E3E-AAF8-38C76E647921 at lifesci.dundee.ac.uk>
Content-Type: text/plain; charset=us-ascii
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
>> _______________________________________________
>> ome-users mailing list
>> ome-users at lists.openmicroscopy.org.uk
>> http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-users
>
>
> The University of Dundee is a registered Scottish Charity, No: SC015096
> _______________________________________________
> ome-users mailing list
> ome-users at lists.openmicroscopy.org.uk
> http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-users
------------------------------
Message: 2
Date: Tue, 16 Dec 2014 15:00:01 +0100
From: Philippe Mailly <philippe.mailly at college-de-france.fr>
To: ome-users at lists.openmicroscopy.org.uk
Subject: [ome-users] Huygens H5
Message-ID: <54903AE1.5060804 at college-de-france.fr>
Content-Type: text/plain; charset="utf-8"; Format="flowed"
Hi,
Is it a LOCI roadmap to read huygens h5 file format ??
Philippe
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Message: 3
Date: Tue, 16 Dec 2014 14:04:00 +0000
From: Mark Carroll <m.t.b.carroll at dundee.ac.uk>
To: <ome-users at lists.openmicroscopy.org.uk>
Subject: Re: [ome-users] Huygens H5
Message-ID: <54903BD0.2050000 at dundee.ac.uk>
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Dear Philippe,
> Is it a LOCI roadmap to read huygens h5 file format ??
We do have a relevant ticket noted at
http://trac.openmicroscopy.org/ome/ticket/4104 and would be glad to add
you, or anybody else interested, to the cc: list so that you receive
updates.
-- Mark
The University of Dundee is a registered Scottish Charity, No: SC015096
------------------------------
Message: 4
Date: Tue, 16 Dec 2014 15:12:54 +0100
From: Niko Ehrenfeuchter <nikolaus.ehrenfeuchter at unibas.ch>
To: ome-users at lists.openmicroscopy.org.uk
Subject: Re: [ome-users] Huygens H5
Message-ID: <54903DE6.5080601 at unibas.ch>
Content-Type: text/plain; charset=ISO-8859-1; format=flowed
Dear Philippe,
as long as BioFormats doesn't read it, at least for Fiji you can work
around it by using the HDF5 plugin provided here:
http://lmb.informatik.uni-freiburg.de/resources/opensource/imagej_plugins/hdf5.html
When importing SVI-HDF5 files with it, make sure to select the image
dataset from the path and check the "individual hyperstacks (custom
layout)" option.
Then put "tczyx" into the "data set layout" field and click "load".
Cheers
Niko
On 16.12.2014 15:04, Mark Carroll wrote:
> Dear Philippe,
>
>> Is it a LOCI roadmap to read huygens h5 file format ??
>
> We do have a relevant ticket noted at
> http://trac.openmicroscopy.org/ome/ticket/4104 and would be glad to add
> you, or anybody else interested, to the cc: list so that you receive
> updates.
>
> -- Mark
>
> The University of Dundee is a registered Scottish Charity, No: SC015096
> _______________________________________________
> ome-users mailing list
> ome-users at lists.openmicroscopy.org.uk
> http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-users
--
Niko Ehrenfeuchter | Image Analysis Specialist | Biozentrum, University
of Basel | Klingelbergstr. 50/70 | CH-4056 Basel
Phone: +41 (61) 26 72673 | nikolaus.ehrenfeuchter at unibas.ch |
www.biozentrum.unibas.ch<http://www.biozentrum.unibas.ch> | www.microscopynetwork.unibas.ch<http://www.microscopynetwork.unibas.ch>
------------------------------
Message: 5
Date: Tue, 16 Dec 2014 16:47:19 +0100
From: Philippe Mailly <philippe.mailly at college-de-france.fr>
To: ome-users at lists.openmicroscopy.org.uk
Subject: [ome-users] Groups visibility
Message-ID: <54905407.90706 at college-de-france.fr>
Content-Type: text/plain; charset="utf-8"; Format="flowed"
Hi,
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 ????
Is it a "special" issue from the web client ?
Philippe
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------------------------------
Message: 6
Date: Tue, 16 Dec 2014 15:52:07 +0000
From: William Moore <will at lifesci.dundee.ac.uk>
To: Philippe Mailly <philippe.mailly at college-de-france.fr>
Cc: ome-users at lists.openmicroscopy.org.uk
Subject: Re: [ome-users] Groups visibility
Message-ID:
<377D5F59-1F97-4DF2-9067-331F9CA6E2A0 at lifesci.dundee.ac.uk>
Content-Type: text/plain; charset=us-ascii
Hi Philippe,
Yes, this feature only exists in web client at the moment.
It is useful for accessing all data that you have permissions to see.
I am not sure whether we are planning to add this to Insight any time soon.
Will.
On 16 Dec 2014, at 15:47, Philippe Mailly <philippe.mailly at college-de-france.fr> wrote:
> Hi,
>
> 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 ????
> Is it a "special" issue from the web client ?
>
> Philippe
>
> <philippe_mailly.vcf>_______________________________________________
> ome-users mailing list
> ome-users at lists.openmicroscopy.org.uk
> http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-users
------------------------------
Message: 7
Date: Tue, 16 Dec 2014 10:19:45 -0600
From: Melissa Linkert <melissa at glencoesoftware.com>
To: FangfeiLi <lifangfei at hotmail.com>
Cc: "ome-users at lists.openmicroscopy.org.uk"
<ome-users at lists.openmicroscopy.org.uk>
Subject: Re: [ome-users] How to get timestamp when using bfconvert
Message-ID: <20141216161945.GA2367 at hera>
Content-Type: text/plain; charset=us-ascii
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
> >> _______________________________________________
> >> ome-users mailing list
> >> ome-users at lists.openmicroscopy.org.uk
> >> http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-users
> >
> >
> > The University of Dundee is a registered Scottish Charity, No: SC015096
> > _______________________________________________
> > ome-users mailing list
> > ome-users at lists.openmicroscopy.org.uk
> > http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-users
>
> _______________________________________________
> ome-users mailing list
> ome-users at lists.openmicroscopy.org.uk
> http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-users
------------------------------
Message: 8
Date: Tue, 16 Dec 2014 14:59:40 -0500
From: FangfeiLi <lifangfei at hotmail.com>
To: melissa at glencoesoftware.com
Cc: "ome-users at lists.openmicroscopy.org.uk"
<ome-users at lists.openmicroscopy.org.uk>
Subject: Re: [ome-users] How to get timestamp when using bfconvert
Message-ID: <BLU436-SMTP514C1BBE2BDE67A97F94DDAE6C0 at phx.gbl>
Content-Type: text/plain; charset="us-ascii"
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
>>>> _______________________________________________
>>>> ome-users mailing list
>>>> ome-users at lists.openmicroscopy.org.uk
>>>> http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-users
>>>
>>>
>>> The University of Dundee is a registered Scottish Charity, No: SC015096
>>> _______________________________________________
>>> ome-users mailing list
>>> ome-users at lists.openmicroscopy.org.uk
>>> http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-users
>>
>> _______________________________________________
>> ome-users mailing list
>> ome-users at lists.openmicroscopy.org.uk
>> http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-users
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Message: 9
Date: Tue, 16 Dec 2014 14:04:30 -0600
From: Curtis Rueden <ctrueden at wisc.edu>
To: FangfeiLi <lifangfei at hotmail.com>
Cc: "ome-users at lists.openmicroscopy.org.uk"
<ome-users at lists.openmicroscopy.org.uk>
Subject: Re: [ome-users] How to get timestamp when using bfconvert
Message-ID:
<CADN69ymQvk+sQP-_KhTRibUDUmEsukjNfRTykMWdthy-qb0e8Q at mail.gmail.com>
Content-Type: text/plain; charset="utf-8"
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
> _______________________________________________
> ome-users mailing list
> ome-users at lists.openmicroscopy.org.uk
> http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-users
>
>
>
> The University of Dundee is a registered Scottish Charity, No: SC015096
> _______________________________________________
> ome-users mailing list
> ome-users at lists.openmicroscopy.org.uk
> http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-users
>
>
> _______________________________________________
> ome-users mailing list
> ome-users at lists.openmicroscopy.org.uk
> http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-users
>
>
>
> _______________________________________________
> ome-users mailing list
> ome-users at lists.openmicroscopy.org.uk
> http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-users
>
>
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