metamorph metadata
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Kyle McQuade
Jun 1, 2015, 6:38:54 PM6/1/15
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I am currently collecting time lapse series with metamorph for cell motility analysis. Icy seems to read the metadata of the tif stacks we collect fine with regards to distance, but it doesn't recognize the time interval.
When I look at the image info in metamorph, I see no information regarding image interval, only the timestamp for when the image was actually collecte (and from which interval can be easily determined, of course). Icy seems unable to interpret the timestamp, and sets the interval to what seems to be a default of 100ms, no matter the actual interval. I know that this can be manually adjusted, but that is easy to forget to do. It's also easy to misenter the interval when your experiments require that you have different intervals for different iterations.
Should I expect Icy to be able to read the time stamp and calculate image interval from it? If not, should the metadata from metamorph include the interval and not just the timestamp?
Any help would be greatly appreciated.
Stephane
Jun 8, 2015, 8:20:28 AM6/8/15
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Hello Kyle,
Icy reads metadata through Bio-Formats so if Bio-Formats can access the metamorph time information we should get it in Icy as well. The problem is that by default Icy do use the "time interval" field which is not always fill or/and can be different from the timestamp information attached to each independent frame. indeed it would be better if metamorph could eventually export the time interval field but we can also make the change in Icy so if we have the timestamp information we automatically calculate the time interval from it when this one is not present.
By the way, you can see all metadata from your image in Icy by clicking on the "Metadata" button in the Sequence Properties part.
Best,
- Stephane
Icy reads metadata through Bio-Formats so if Bio-Formats can access the metamorph time information we should get it in Icy as well. The problem is that by default Icy do use the "time interval" field which is not always fill or/and can be different from the timestamp information attached to each independent frame. indeed it would be better if metamorph could eventually export the time interval field but we can also make the change in Icy so if we have the timestamp information we automatically calculate the time interval from it when this one is not present.
By the way, you can see all metadata from your image in Icy by clicking on the "Metadata" button in the Sequence Properties part.
Best,
- Stephane
Curtis Rueden
Jun 8, 2015, 12:33:12 PM6/8/15
to icy-software, kylejm...@gmail.com
Hi Stephane,
> we can also make the change in Icy so if we have the timestamp
> information we automatically calculate the time interval from it when
> this one is not present.
FWIW, this is what the Bio-Formats ImageJ plugin does [1, 2].
Regards,
Curtis
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Stephane
Jun 9, 2015, 3:50:54 AM6/9/15
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Hi Curtis,
Yeah that makes sense, I guess it's better to have an estimation than nothing or an invalid value. Thanks for pointing that out :)
Best,
- Stephane
Yeah that makes sense, I guess it's better to have an estimation than nothing or an invalid value. Thanks for pointing that out :)
Best,
- Stephane
Le lundi 8 juin 2015 18:33:12 UTC+2, Curtis Rueden a écrit :
Hi Stephane,> we can also make the change in Icy so if we have the timestamp> information we automatically calculate the time interval from it when> this one is not present.FWIW, this is what the Bio-Formats ImageJ plugin does [1, 2].Regards,Curtis
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