metadata and time depiction

[fabrice senger-2]

as follow up to a previous mail, i just wonder why the time dimension is
always depicted as t (time frame) and not in real units as sec.
Indeed, using the LOCI plugin it is possible to retrieve metadata from
almost every format.

Thus it would be interesting to have direct acces to those parameters.

As example, if you do time-lapse and have to pause your acquisition for one
or two acquisition, you could not use the time interval, but the metadata
acqusitionTime is still relevant.

Thank you,

Fabrice.

[ctrueden]

Hi Fabrice,

as follow up to a previous mail, i just wonder why the time dimension is
> always depicted as t (time frame) and not in real units as sec.
> Indeed, using the LOCI plugin it is possible to retrieve metadata from
> almost every format.
>

The Bio-Formats Importer does populate the frame interval in the image
properties when that information is available. In the case of variable time
between frames, we average the times and populate the frame interval with
the mean (though the eventual goal is for ImageJ to support variable time
frames directly). And I believe that in general, ImageJ uses the frame
interval value for the frames per second when animating—adjustable by right
clicking the Play button next to the time slider.

Thus it would be interesting to have direct acces to those parameters.
>

Are you suggesting that you would like to see the timestamp in seconds
displayed as part of the label at the top of the image window?

As example, if you do time-lapse and have to pause your acquisition for one
> or two acquisition, you could not use the time interval, but the metadata
> acqusitionTime is still relevant.
>

Whether such a pause is properly recorded in the metadata depends on the
file format. As I said above, Bio-Formats averages the timestamps, so you
should still get a reasonable frame interval in the properties, as long as
the correct values are really present in metadata.

-Curtis

On Thu, Aug 26, 2010 at 5:48 AM, fabrice senger <[hidden email]>wrote:

> as follow up to a previous mail, i just wonder why the time dimension is
> always depicted as t (time frame) and not in real units as sec.
> Indeed, using the LOCI plugin it is possible to retrieve metadata from
> almost every format.
>
> Thus it would be interesting to have direct acces to those parameters.
>
> As example, if you do time-lapse and have to pause your acquisition for one
> or two acquisition, you could not use the time interval, but the metadata
> acqusitionTime is still relevant.
>
> Thank you,
>
> Fabrice.
>

[fabrice senger-2]

Hello,

I had such a piece of discussion off-list with Dan White.
As I work with stk files, i have access to the image creation time (this is
accurate even you pause the acquisition), I have access to this info with
the LOCI plugin and some code Melissa kindly sent me.

What would be of interest is a tool like a time slider as you can get it in
Metamorph or in Imaris...or then : "

> Are you suggesting that you would like to see the timestamp in seconds
> displayed as part of the label at the top of the image window?"
>



This is probably a particular situation when you have to pause acquisition
for one or two acquisitions but in this case dynamic measurements would not
be accurate if based on time intervals (?!)

Thank you for your reply,

Best,

Fabrice.

2010/8/26 Curtis Rueden <[hidden email]>

> Hi Fabrice,
>
> as follow up to a previous mail, i just wonder why the time dimension is
> > always depicted as t (time frame) and not in real units as sec.
> > Indeed, using the LOCI plugin it is possible to retrieve metadata from
> > almost every format.
> >
>
> The Bio-Formats Importer does populate the frame interval in the image
> properties when that information is available. In the case of variable time
> between frames, we average the times and populate the frame interval with
> the mean (though the eventual goal is for ImageJ to support variable time
> frames directly). And I believe that in general, ImageJ uses the frame
> interval value for the frames per second when animating—adjustable by right
> clicking the Play button next to the time slider.
>
> Thus it would be interesting to have direct acces to those parameters.
> >
>
> Are you suggesting that you would like to see the timestamp in seconds
> displayed as part of the label at the top of the image window?
>

Yes this is what I think about!

>
> As example, if you do time-lapse and have to pause your acquisition for one
> > or two acquisition, you could not use the time interval, but the metadata
> > acqusitionTime is still relevant.
> >
>
> Whether such a pause is properly recorded in the metadata depends on the
> file format. As I said above, Bio-Formats averages the timestamps, so you
> should still get a reasonable frame interval in the properties, as long as
> the correct values are really present in metadata.
>
> -Curtis
>
> On Thu, Aug 26, 2010 at 5:48 AM, fabrice senger <[hidden email]
> >wrote:
>
> > as follow up to a previous mail, i just wonder why the time dimension is
> > always depicted as t (time frame) and not in real units as sec.
> > Indeed, using the LOCI plugin it is possible to retrieve metadata from
> > almost every format.
> >
> > Thus it would be interesting to have direct acces to those parameters.
> >
> > As example, if you do time-lapse and have to pause your acquisition for
> one
> > or two acquisition, you could not use the time interval, but the metadata
> > acqusitionTime is still relevant.
> >
> > Thank you,
> >
> > Fabrice.
> >
>

[vs11]

Hi all,
I use Metamorph too and have data sets up to 20gb and find it
Difficult to find time stamps specially after making a maximum projection of the z stacks. Would love to know how you are using loci plugin to get the time stamp! I am not familiar with programing but I do have the loci plugin installed would love a fix I could apply without having to write codes
Thanks
Vinay

Vinay Singh
4315 FFSC, Duke university
Durham NC 27708
919-6134456

On Aug 27, 2010, at 3:05 AM, fabrice senger <[hidden email]> wrote:

> Hello,
>
> I had such a piece of discussion off-list with Dan White.
> As I work with stk files, i have access to the image creation time (this is
> accurate even you pause the acquisition), I have access to this info with
> the LOCI plugin and some code Melissa kindly sent me.
>
> What would be of interest is a tool like a time slider as you can get it in
> Metamorph or in Imaris...or then : "
>
>> Are you suggesting that you would like to see the timestamp in seconds
>> displayed as part of the label at the top of the image window?"
>>
>
>
>
> This is probably a particular situation when you have to pause acquisition
> for one or two acquisitions but in this case dynamic measurements would not
> be accurate if based on time intervals (?!)
>
> Thank you for your reply,
>
> Best,
>
> Fabrice.
>
> 2010/8/26 Curtis Rueden <[hidden email]>
>
>> Hi Fabrice,
>>
>> as follow up to a previous mail, i just wonder why the time dimension is
>>> always depicted as t (time frame) and not in real units as sec.
>>> Indeed, using the LOCI plugin it is possible to retrieve metadata from
>>> almost every format.
>>>
>>
>> The Bio-Formats Importer does populate the frame interval in the image
>> properties when that information is available. In the case of variable time
>> between frames, we average the times and populate the frame interval with
>> the mean (though the eventual goal is for ImageJ to support variable time
>> frames directly). And I believe that in general, ImageJ uses the frame
>> interval value for the frames per second when animating—adjustable by right
>> clicking the Play button next to the time slider.
>>
>> Thus it would be interesting to have direct acces to those parameters.
>>>
>>
>> Are you suggesting that you would like to see the timestamp in seconds
>> displayed as part of the label at the top of the image window?
>>
>
> Yes this is what I think about!
>
>>
>> As example, if you do time-lapse and have to pause your acquisition for one
>>> or two acquisition, you could not use the time interval, but the metadata
>>> acqusitionTime is still relevant.
>>>
>>
>> Whether such a pause is properly recorded in the metadata depends on the
>> file format. As I said above, Bio-Formats averages the timestamps, so you
>> should still get a reasonable frame interval in the properties, as long as
>> the correct values are really present in metadata.
>>
>> -Curtis
>>
>> On Thu, Aug 26, 2010 at 5:48 AM, fabrice senger <[hidden email]
>>> wrote:
>>
>>> as follow up to a previous mail, i just wonder why the time dimension is
>>> always depicted as t (time frame) and not in real units as sec.
>>> Indeed, using the LOCI plugin it is possible to retrieve metadata from
>>> almost every format.
>>>
>>> Thus it would be interesting to have direct acces to those parameters.
>>>
>>> As example, if you do time-lapse and have to pause your acquisition for
>> one
>>> or two acquisition, you could not use the time interval, but the metadata
>>> acqusitionTime is still relevant.
>>>
>>> Thank you,
>>>
>>> Fabrice.
>>>
>>

[fabrice senger-2]

Hi there,

I hope it's not to boring, I'm still working on file metadata (stk and nd
folders as ganerated by Metamorph).
This time i open my files with the LOCI plugin and ask for the metadata
depicted in the result table...In my case I would have been happy to get the
Results table and not the "Original Metada - filename"...with the Results
table I would have been able to extract whatever info to a custom table.

So i tried to rename the Original-Metadta- table to Results, but this
doesn't work in my hands...

Any clue ?

Thank you very much,

Fabrice.


2010/8/27 Vinay Singh <[hidden email]>

> Hi all,
> I use Metamorph too and have data sets up to 20gb and find it
> Difficult to find time stamps specially after making a maximum projection
> of the z stacks. Would love to know how you are using loci plugin to get the
> time stamp! I am not familiar with programing but I do have the loci plugin
> installed would love a fix I could apply without having to write codes
> Thanks
> Vinay
>
> Vinay Singh
> 4315 FFSC, Duke university
> Durham NC 27708
> 919-6134456
>
> On Aug 27, 2010, at 3:05 AM, fabrice senger <[hidden email]>
> wrote:
>
> > Hello,
> >
> > I had such a piece of discussion off-list with Dan White.
> > As I work with stk files, i have access to the image creation time (this
> is
> > accurate even you pause the acquisition), I have access to this info with
> > the LOCI plugin and some code Melissa kindly sent me.
> >
> > What would be of interest is a tool like a time slider as you can get it
> in
> > Metamorph or in Imaris...or then : "
> >
> >> Are you suggesting that you would like to see the timestamp in seconds
> >> displayed as part of the label at the top of the image window?"
> >>
> >
> >
> >
> > This is probably a particular situation when you have to pause
> acquisition
> > for one or two acquisitions but in this case dynamic measurements would
> not
> > be accurate if based on time intervals (?!)
> >
> > Thank you for your reply,
> >
> > Best,
> >
> > Fabrice.
> >
> > 2010/8/26 Curtis Rueden <[hidden email]>
> >
> >> Hi Fabrice,
> >>
> >> as follow up to a previous mail, i just wonder why the time dimension is
> >>> always depicted as t (time frame) and not in real units as sec.
> >>> Indeed, using the LOCI plugin it is possible to retrieve metadata from
> >>> almost every format.
> >>>
> >>
> >> The Bio-Formats Importer does populate the frame interval in the image
> >> properties when that information is available. In the case of variable
> time
> >> between frames, we average the times and populate the frame interval
> with
> >> the mean (though the eventual goal is for ImageJ to support variable
> time
> >> frames directly). And I believe that in general, ImageJ uses the frame
> >> interval value for the frames per second when animating—adjustable by
> right
> >> clicking the Play button next to the time slider.
> >>
> >> Thus it would be interesting to have direct acces to those parameters.
> >>>
> >>
> >> Are you suggesting that you would like to see the timestamp in seconds
> >> displayed as part of the label at the top of the image window?
> >>
> >
> > Yes this is what I think about!
> >
> >>
> >> As example, if you do time-lapse and have to pause your acquisition for
> one
> >>> or two acquisition, you could not use the time interval, but the
> metadata
> >>> acqusitionTime is still relevant.
> >>>
> >>
> >> Whether such a pause is properly recorded in the metadata depends on the
> >> file format. As I said above, Bio-Formats averages the timestamps, so
> you
> >> should still get a reasonable frame interval in the properties, as long
> as
> >> the correct values are really present in metadata.
> >>
> >> -Curtis
> >>
> >> On Thu, Aug 26, 2010 at 5:48 AM, fabrice senger <
> [hidden email]
> >>> wrote:
> >>
> >>> as follow up to a previous mail, i just wonder why the time dimension
> is
> >>> always depicted as t (time frame) and not in real units as sec.
> >>> Indeed, using the LOCI plugin it is possible to retrieve metadata from
> >>> almost every format.
> >>>
> >>> Thus it would be interesting to have direct acces to those parameters.
> >>>
> >>> As example, if you do time-lapse and have to pause your acquisition for
> >> one
> >>> or two acquisition, you could not use the time interval, but the
> metadata
> >>> acqusitionTime is still relevant.
> >>>
> >>> Thank you,
> >>>
> >>> Fabrice.
> >>>
> >>
>

[fabrice senger-2]

In addition to this mail : when I try to acces creation date a message
appears in the IJ bar :

"unknown creation date format : 20100722 14:53:38.88"

and when I import my image with metadata in a result window, save that table
and then reopen it using import results, the table wich opens is still not a
Results table...and I can not access it (?!)


2010/8/30 fabrice senger <[hidden email]>

> Hi there,
>
> I hope it's not to boring, I'm still working on file metadata (stk and nd
> folders as ganerated by Metamorph).
> This time i open my files with the LOCI plugin and ask for the metadata
> depicted in the result table...In my case I would have been happy to get the
> Results table and not the "Original Metada - filename"...with the Results
> table I would have been able to extract whatever info to a custom table.
>
> So i tried to rename the Original-Metadta- table to Results, but this
> doesn't work in my hands...
>
> Any clue ?
>
> Thank you very much,
>
> Fabrice.
>
>
> 2010/8/27 Vinay Singh <[hidden email]>
>
> Hi all,
>> I use Metamorph too and have data sets up to 20gb and find it
>> Difficult to find time stamps specially after making a maximum projection
>> of the z stacks. Would love to know how you are using loci plugin to get the
>> time stamp! I am not familiar with programing but I do have the loci plugin
>> installed would love a fix I could apply without having to write codes
>> Thanks
>> Vinay
>>
>> Vinay Singh
>> 4315 FFSC, Duke university
>> Durham NC 27708
>> 919-6134456
>>
>> On Aug 27, 2010, at 3:05 AM, fabrice senger <[hidden email]>
>> wrote:
>>
>> > Hello,
>> >
>> > I had such a piece of discussion off-list with Dan White.
>> > As I work with stk files, i have access to the image creation time (this
>> is
>> > accurate even you pause the acquisition), I have access to this info
>> with
>> > the LOCI plugin and some code Melissa kindly sent me.
>> >
>> > What would be of interest is a tool like a time slider as you can get it
>> in
>> > Metamorph or in Imaris...or then : "
>> >
>> >> Are you suggesting that you would like to see the timestamp in seconds
>> >> displayed as part of the label at the top of the image window?"
>> >>
>> >
>> >
>> >
>> > This is probably a particular situation when you have to pause
>> acquisition
>> > for one or two acquisitions but in this case dynamic measurements would
>> not
>> > be accurate if based on time intervals (?!)
>> >
>> > Thank you for your reply,
>> >
>> > Best,
>> >
>> > Fabrice.
>> >
>> > 2010/8/26 Curtis Rueden <[hidden email]>
>> >
>> >> Hi Fabrice,
>> >>
>> >> as follow up to a previous mail, i just wonder why the time dimension
>> is
>> >>> always depicted as t (time frame) and not in real units as sec.
>> >>> Indeed, using the LOCI plugin it is possible to retrieve metadata from
>> >>> almost every format.
>> >>>
>> >>
>> >> The Bio-Formats Importer does populate the frame interval in the image
>> >> properties when that information is available. In the case of variable
>> time
>> >> between frames, we average the times and populate the frame interval
>> with
>> >> the mean (though the eventual goal is for ImageJ to support variable
>> time
>> >> frames directly). And I believe that in general, ImageJ uses the frame
>> >> interval value for the frames per second when animating—adjustable by
>> right
>> >> clicking the Play button next to the time slider.
>> >>
>> >> Thus it would be interesting to have direct acces to those parameters.
>> >>>
>> >>
>> >> Are you suggesting that you would like to see the timestamp in seconds
>> >> displayed as part of the label at the top of the image window?
>> >>
>> >
>> > Yes this is what I think about!
>> >
>> >>
>> >> As example, if you do time-lapse and have to pause your acquisition for
>> one
>> >>> or two acquisition, you could not use the time interval, but the
>> metadata
>> >>> acqusitionTime is still relevant.
>> >>>
>> >>
>> >> Whether such a pause is properly recorded in the metadata depends on
>> the
>> >> file format. As I said above, Bio-Formats averages the timestamps, so
>> you
>> >> should still get a reasonable frame interval in the properties, as long
>> as
>> >> the correct values are really present in metadata.
>> >>
>> >> -Curtis
>> >>
>> >> On Thu, Aug 26, 2010 at 5:48 AM, fabrice senger <
>> [hidden email]
>> >>> wrote:
>> >>
>> >>> as follow up to a previous mail, i just wonder why the time dimension
>> is
>> >>> always depicted as t (time frame) and not in real units as sec.
>> >>> Indeed, using the LOCI plugin it is possible to retrieve metadata from
>> >>> almost every format.
>> >>>
>> >>> Thus it would be interesting to have direct acces to those parameters.
>> >>>
>> >>> As example, if you do time-lapse and have to pause your acquisition
>> for
>> >> one
>> >>> or two acquisition, you could not use the time interval, but the
>> metadata
>> >>> acqusitionTime is still relevant.
>> >>>
>> >>> Thank you,
>> >>>
>> >>> Fabrice.
>> >>>
>> >>
>>
>
>

[Rasband, Wayne (NIH/NIMH) [E]]

On Aug 30, 2010, at 5:06 AM, fabrice senger wrote:

> In addition to this mail : when I try to acces creation date a message
> appears in the IJ bar :
>
> "unknown creation date format : 20100722 14:53:38.88"
>
> and when I import my image with metadata in a result window, save that table
> and then reopen it using import results, the table wich opens is still not a
> Results table...and I can not access it (?!)

You can get all the metadata, as a string, of images imported with the Bio-Formats plugin using the getMetadata("info") macro function. In the ImageJ 1.44g daily build, you can retrieve specified metadata values using the getInfo() macro function. For example:

   order = getInfo("DimensionOrder");
   type = getInfo("PixelType");
   sizeC = getInfo("SizeC");

The getInfo() function can also retrieve the value of DICOM tags

   modality = getInfo("0008,0060");
   sliceThickness = getInfo("0018,0050");
   position = getInfo("0020,0032");

and Java properties

   version = getInfo("java.version");
   os = getInfo("os.name");
   home = getInfo("user.home");

-wayne

>> Hi there,
>>
>> I hope it's not to boring, I'm still working on file metadata (stk and nd
>> folders as ganerated by Metamorph).
>> This time i open my files with the LOCI plugin and ask for the metadata
>> depicted in the result table...In my case I would have been happy to get the
>> Results table and not the "Original Metada - filename"...with the Results
>> table I would have been able to extract whatever info to a custom table.
>>
>> So i tried to rename the Original-Metadta- table to Results, but this
>> doesn't work in my hands...
>>
>> Any clue ?
>>
>> Thank you very much,
>>
>> Fabrice.
>>
>>
>> 2010/8/27 Vinay Singh <[hidden email]>
>>
>> Hi all,
>>> I use Metamorph too and have data sets up to 20gb and find it
>>> Difficult to find time stamps specially after making a maximum projection
>>> of the z stacks. Would love to know how you are using loci plugin to get the
>>> time stamp! I am not familiar with programing but I do have the loci plugin
>>> installed would love a fix I could apply without having to write codes
>>> Thanks
>>> Vinay
>>>
>>> Vinay Singh
>>> 4315 FFSC, Duke university
>>> Durham NC 27708
>>> 919-6134456
>>>
>>> On Aug 27, 2010, at 3:05 AM, fabrice senger <[hidden email]>
>>> wrote:
>>>
>>>> Hello,
>>>>
>>>> I had such a piece of discussion off-list with Dan White.
>>>> As I work with stk files, i have access to the image creation time (this
>>> is
>>>> accurate even you pause the acquisition), I have access to this info
>>> with
>>>> the LOCI plugin and some code Melissa kindly sent me.
>>>>
>>>> What would be of interest is a tool like a time slider as you can get it
>>> in
>>>> Metamorph or in Imaris...or then : "
>>>>
>>>>> Are you suggesting that you would like to see the timestamp in seconds
>>>>> displayed as part of the label at the top of the image window?"
>>>>>
>>>>
>>>>
>>>>
>>>> This is probably a particular situation when you have to pause
>>> acquisition
>>>> for one or two acquisitions but in this case dynamic measurements would
>>> not
>>>> be accurate if based on time intervals (?!)
>>>>
>>>> Thank you for your reply,
>>>>
>>>> Best,
>>>>
>>>> Fabrice.
>>>>
>>>> 2010/8/26 Curtis Rueden <[hidden email]>
>>>>
>>>>> Hi Fabrice,
>>>>>
>>>>> as follow up to a previous mail, i just wonder why the time dimension
>>> is
>>>>>> always depicted as t (time frame) and not in real units as sec.
>>>>>> Indeed, using the LOCI plugin it is possible to retrieve metadata from
>>>>>> almost every format.
>>>>>>
>>>>>
>>>>> The Bio-Formats Importer does populate the frame interval in the image
>>>>> properties when that information is available. In the case of variable
>>> time
>>>>> between frames, we average the times and populate the frame interval
>>> with
>>>>> the mean (though the eventual goal is for ImageJ to support variable
>>> time
>>>>> frames directly). And I believe that in general, ImageJ uses the frame
>>>>> interval value for the frames per second when animating—adjustable by
>>> right
>>>>> clicking the Play button next to the time slider.
>>>>>
>>>>> Thus it would be interesting to have direct acces to those parameters.
>>>>>>
>>>>>
>>>>> Are you suggesting that you would like to see the timestamp in seconds
>>>>> displayed as part of the label at the top of the image window?
>>>>>
>>>>
>>>> Yes this is what I think about!
>>>>
>>>>>
>>>>> As example, if you do time-lapse and have to pause your acquisition for
>>> one
>>>>>> or two acquisition, you could not use the time interval, but the
>>> metadata
>>>>>> acqusitionTime is still relevant.
>>>>>>
>>>>>
>>>>> Whether such a pause is properly recorded in the metadata depends on
>>> the
>>>>> file format. As I said above, Bio-Formats averages the timestamps, so
>>> you
>>>>> should still get a reasonable frame interval in the properties, as long
>>> as
>>>>> the correct values are really present in metadata.
>>>>>
>>>>> -Curtis
>>>>>
>>>>> On Thu, Aug 26, 2010 at 5:48 AM, fabrice senger <
>>> [hidden email]
>>>>>> wrote:
>>>>>
>>>>>> as follow up to a previous mail, i just wonder why the time dimension
>>> is
>>>>>> always depicted as t (time frame) and not in real units as sec.
>>>>>> Indeed, using the LOCI plugin it is possible to retrieve metadata from
>>>>>> almost every format.
>>>>>>
>>>>>> Thus it would be interesting to have direct acces to those parameters.
>>>>>>
>>>>>> As example, if you do time-lapse and have to pause your acquisition
>>> for
>>>>> one
>>>>>> or two acquisition, you could not use the time interval, but the
>>> metadata
>>>>>> acqusitionTime is still relevant.
>>>>>>
>>>>>> Thank you,
>>>>>>
>>>>>> Fabrice.
>>>>>>
>>>>>
>>>
>>
>>

[fabrice senger-2]

Hello,

and thank you for the reply.
I use the latest build 1.44G3 (daily build)...
I do not have any problem to access the metadata, with the LOCI plugin
(really great) I can access all the data from my Metamorph files (as I deal
with those) BUT, I couldn't manage to manipulate those datas...This is all
about time-lapse experiments and the ability to use the time data generated
by Metamorph...more over I worked a lot with G. Carpentiers TabStatCustom
Results : you can manipulate the Results table and generate a new custom
table but now, from LOCI I get a table called "Original Metadata -
"filename"", and it is stated I should be able to save this table and
re-open it as a regular Results Table, and I can not manage to do so...

To get around this I can of course export the whole stuff to excel ...

2010/8/31 Rasband, Wayne (NIH/NIMH) [E] <[hidden email]>

> On Aug 30, 2010, at 5:06 AM, fabrice senger wrote:
>
> > In addition to this mail : when I try to acces creation date a message
> > appears in the IJ bar :
> >
> > "unknown creation date format : 20100722 14:53:38.88"
> >
> > and when I import my image with metadata in a result window, save that
> table
> > and then reopen it using import results, the table wich opens is still
> not a
> > Results table...and I can not access it (?!)
>
> You can get all the metadata, as a string, of images imported with the
> Bio-Formats plugin using the getMetadata("info") macro function. In the
> ImageJ 1.44g daily build, you can retrieve specified metadata values using
> the getInfo() macro function. For example:
>
>   order = getInfo("DimensionOrder");
>   type = getInfo("PixelType");
>   sizeC = getInfo("SizeC");
>
> The getInfo() function can also retrieve the value of DICOM tags
>
>   modality = getInfo("0008,0060");
>   sliceThickness = getInfo("0018,0050");
>   position = getInfo("0020,0032");
>
> and Java properties
>
>   version = getInfo("java.version");
>   os = getInfo("os.name");
>   home = getInfo("user.home");
>
> -wayne
>
>
> >> Hi there,
> >>
> >> I hope it's not to boring, I'm still working on file metadata (stk and
> nd
> >> folders as ganerated by Metamorph).
> >> This time i open my files with the LOCI plugin and ask for the metadata
> >> depicted in the result table...In my case I would have been happy to get
> the
> >> Results table and not the "Original Metada - filename"...with the
> Results
> >> table I would have been able to extract whatever info to a custom table.
> >>
> >> So i tried to rename the Original-Metadta- table to Results, but this
> >> doesn't work in my hands...
> >>
> >> Any clue ?
> >>
> >> Thank you very much,
> >>
> >> Fabrice.
> >>
> >>
> >> 2010/8/27 Vinay Singh <[hidden email]>
> >>
> >> Hi all,
> >>> I use Metamorph too and have data sets up to 20gb and find it
> >>> Difficult to find time stamps specially after making a maximum
> projection
> >>> of the z stacks. Would love to know how you are using loci plugin to
> get the
> >>> time stamp! I am not familiar with programing but I do have the loci
> plugin
> >>> installed would love a fix I could apply without having to write codes
> >>> Thanks
> >>> Vinay
> >>>
> >>> Vinay Singh
> >>> 4315 FFSC, Duke university
> >>> Durham NC 27708
> >>> 919-6134456
> >>>
> >>> On Aug 27, 2010, at 3:05 AM, fabrice senger <[hidden email]>
> >>> wrote:
> >>>
> >>>> Hello,
> >>>>
> >>>> I had such a piece of discussion off-list with Dan White.
> >>>> As I work with stk files, i have access to the image creation time
> (this
> >>> is
> >>>> accurate even you pause the acquisition), I have access to this info
> >>> with
> >>>> the LOCI plugin and some code Melissa kindly sent me.
> >>>>
> >>>> What would be of interest is a tool like a time slider as you can get
> it
> >>> in
> >>>> Metamorph or in Imaris...or then : "
> >>>>
> >>>>> Are you suggesting that you would like to see the timestamp in
> seconds
> >>>>> displayed as part of the label at the top of the image window?"
> >>>>>
> >>>>
> >>>>
> >>>>
> >>>> This is probably a particular situation when you have to pause
> >>> acquisition
> >>>> for one or two acquisitions but in this case dynamic measurements
> would
> >>> not
> >>>> be accurate if based on time intervals (?!)
> >>>>
> >>>> Thank you for your reply,
> >>>>
> >>>> Best,
> >>>>
> >>>> Fabrice.
> >>>>
> >>>> 2010/8/26 Curtis Rueden <[hidden email]>
> >>>>
> >>>>> Hi Fabrice,
> >>>>>
> >>>>> as follow up to a previous mail, i just wonder why the time dimension
> >>> is
> >>>>>> always depicted as t (time frame) and not in real units as sec.
> >>>>>> Indeed, using the LOCI plugin it is possible to retrieve metadata
> from
> >>>>>> almost every format.
> >>>>>>
> >>>>>
> >>>>> The Bio-Formats Importer does populate the frame interval in the
> image
> >>>>> properties when that information is available. In the case of
> variable
> >>> time
> >>>>> between frames, we average the times and populate the frame interval
> >>> with
> >>>>> the mean (though the eventual goal is for ImageJ to support variable
> >>> time
> >>>>> frames directly). And I believe that in general, ImageJ uses the
> frame
> >>>>> interval value for the frames per second when animating—adjustable by
> >>> right
> >>>>> clicking the Play button next to the time slider.
> >>>>>
> >>>>> Thus it would be interesting to have direct acces to those
> parameters.
> >>>>>>
> >>>>>
> >>>>> Are you suggesting that you would like to see the timestamp in
> seconds
> >>>>> displayed as part of the label at the top of the image window?
> >>>>>
> >>>>
> >>>> Yes this is what I think about!
> >>>>
> >>>>>
> >>>>> As example, if you do time-lapse and have to pause your acquisition
> for
> >>> one
> >>>>>> or two acquisition, you could not use the time interval, but the
> >>> metadata
> >>>>>> acqusitionTime is still relevant.
> >>>>>>
> >>>>>
> >>>>> Whether such a pause is properly recorded in the metadata depends on
> >>> the
> >>>>> file format. As I said above, Bio-Formats averages the timestamps, so
> >>> you
> >>>>> should still get a reasonable frame interval in the properties, as
> long
> >>> as
> >>>>> the correct values are really present in metadata.
> >>>>>
> >>>>> -Curtis
> >>>>>
> >>>>> On Thu, Aug 26, 2010 at 5:48 AM, fabrice senger <
> >>> [hidden email]
> >>>>>> wrote:
> >>>>>
> >>>>>> as follow up to a previous mail, i just wonder why the time
> dimension
> >>> is
> >>>>>> always depicted as t (time frame) and not in real units as sec.
> >>>>>> Indeed, using the LOCI plugin it is possible to retrieve metadata
> from
> >>>>>> almost every format.
> >>>>>>
> >>>>>> Thus it would be interesting to have direct acces to those
> parameters.
> >>>>>>
> >>>>>> As example, if you do time-lapse and have to pause your acquisition
> >>> for
> >>>>> one
> >>>>>> or two acquisition, you could not use the time interval, but the
> >>> metadata
> >>>>>> acqusitionTime is still relevant.
> >>>>>>
> >>>>>> Thank you,
> >>>>>>
> >>>>>> Fabrice.
> >>>>>>
> >>>>>
> >>>
> >>
> >>
>

[Melissa Linkert-2]

Hi Fabrice,

> In addition to this mail : when I try to acces creation date a message
> appears in the IJ bar :
>
> "unknown creation date format : 20100722 14:53:38.88"

This error was fixed in a relatively recent trunk build of Bio-Formats.
Can you please try updating to the latest trunk build?

Regards,
-Melissa

On Mon, Aug 30, 2010 at 11:06:01AM +0200, fabrice senger wrote:

> In addition to this mail : when I try to acces creation date a message
> appears in the IJ bar :
>
> "unknown creation date format : 20100722 14:53:38.88"
>
> and when I import my image with metadata in a result window, save that table
> and then reopen it using import results, the table wich opens is still not a
> Results table...and I can not access it (?!)
>
>
> 2010/8/30 fabrice senger <[hidden email]>
>
> > Hi there,
> >
> > I hope it's not to boring, I'm still working on file metadata (stk and nd
> > folders as ganerated by Metamorph).
> > This time i open my files with the LOCI plugin and ask for the metadata
> > depicted in the result table...In my case I would have been happy to get the
> > Results table and not the "Original Metada - filename"...with the Results
> > table I would have been able to extract whatever info to a custom table.
> >
> > So i tried to rename the Original-Metadta- table to Results, but this
> > doesn't work in my hands...
> >
> > Any clue ?
> >
> > Thank you very much,
> >
> > Fabrice.
> >
> >
> > 2010/8/27 Vinay Singh <[hidden email]>
> >
> > Hi all,
> >> I use Metamorph too and have data sets up to 20gb and find it
> >> Difficult to find time stamps specially after making a maximum projection
> >> of the z stacks. Would love to know how you are using loci plugin to get the
> >> time stamp! I am not familiar with programing but I do have the loci plugin
> >> installed would love a fix I could apply without having to write codes
> >> Thanks
> >> Vinay
> >>
> >> Vinay Singh
> >> 4315 FFSC, Duke university
> >> Durham NC 27708
> >> 919-6134456
> >>
> >> On Aug 27, 2010, at 3:05 AM, fabrice senger <[hidden email]>
> >> wrote:
> >>
> >> > Hello,
> >> >
> >> > I had such a piece of discussion off-list with Dan White.
> >> > As I work with stk files, i have access to the image creation time (this
> >> is
> >> > accurate even you pause the acquisition), I have access to this info
> >> with
> >> > the LOCI plugin and some code Melissa kindly sent me.
> >> >
> >> > What would be of interest is a tool like a time slider as you can get it
> >> in
> >> > Metamorph or in Imaris...or then : "
> >> >
> >> >> Are you suggesting that you would like to see the timestamp in seconds
> >> >> displayed as part of the label at the top of the image window?"
> >> >>
> >> >
> >> >
> >> >
> >> > This is probably a particular situation when you have to pause
> >> acquisition
> >> > for one or two acquisitions but in this case dynamic measurements would
> >> not
> >> > be accurate if based on time intervals (?!)
> >> >
> >> > Thank you for your reply,
> >> >
> >> > Best,
> >> >
> >> > Fabrice.
> >> >
> >> > 2010/8/26 Curtis Rueden <[hidden email]>
> >> >
> >> >> Hi Fabrice,
> >> >>
> >> >> as follow up to a previous mail, i just wonder why the time dimension
> >> is
> >> >>> always depicted as t (time frame) and not in real units as sec.
> >> >>> Indeed, using the LOCI plugin it is possible to retrieve metadata from
> >> >>> almost every format.
> >> >>>
> >> >>
> >> >> The Bio-Formats Importer does populate the frame interval in the image
> >> >> properties when that information is available. In the case of variable
> >> time
> >> >> between frames, we average the times and populate the frame interval
> >> with
> >> >> the mean (though the eventual goal is for ImageJ to support variable
> >> time
> >> >> frames directly). And I believe that in general, ImageJ uses the frame
> >> >> interval value for the frames per second when animating—adjustable by
> >> right
> >> >> clicking the Play button next to the time slider.
> >> >>
> >> >> Thus it would be interesting to have direct acces to those parameters.
> >> >>>
> >> >>
> >> >> Are you suggesting that you would like to see the timestamp in seconds
> >> >> displayed as part of the label at the top of the image window?
> >> >>
> >> >
> >> > Yes this is what I think about!
> >> >
> >> >>
> >> >> As example, if you do time-lapse and have to pause your acquisition for
> >> one
> >> >>> or two acquisition, you could not use the time interval, but the
> >> metadata
> >> >>> acqusitionTime is still relevant.
> >> >>>
> >> >>
> >> >> Whether such a pause is properly recorded in the metadata depends on
> >> the
> >> >> file format. As I said above, Bio-Formats averages the timestamps, so
> >> you
> >> >> should still get a reasonable frame interval in the properties, as long
> >> as
> >> >> the correct values are really present in metadata.
> >> >>
> >> >> -Curtis
> >> >>
> >> >> On Thu, Aug 26, 2010 at 5:48 AM, fabrice senger <
> >> [hidden email]
> >> >>> wrote:
> >> >>
> >> >>> as follow up to a previous mail, i just wonder why the time dimension
> >> is
> >> >>> always depicted as t (time frame) and not in real units as sec.
> >> >>> Indeed, using the LOCI plugin it is possible to retrieve metadata from
> >> >>> almost every format.
> >> >>>
> >> >>> Thus it would be interesting to have direct acces to those parameters.
> >> >>>
> >> >>> As example, if you do time-lapse and have to pause your acquisition
> >> for
> >> >> one
> >> >>> or two acquisition, you could not use the time interval, but the
> >> metadata
> >> >>> acqusitionTime is still relevant.
> >> >>>
> >> >>> Thank you,
> >> >>>
> >> >>> Fabrice.
> >> >>>
> >> >>
> >>
> >
> >