Save Standard Tiffs

classic Classic list List threaded Threaded
5 messages Options
Reply | Threaded
Open this post in threaded view
|  
Report Content as Inappropriate

Save Standard Tiffs

nranthony
Hi all, I hope the egg nog flows well ;)

I was wondering if there's a way to save standard tiff stacks from MM?  While I love the open-source-ness and complete flexibility of the ome.tifs, I find they're slower to work with and simply end up adding steps to my analyses.

I'd love the option to save:
rootName_ch#_timePnt#_Pos#_[etc.]_.tif
the underscore separated increments would match the multidimensional acquisition I'm guessing...

The only thing that would be missing would be the z-step size for my purposes, but that could be pulled from the metadata txt, right?

Thanks in advance for your time.

Neil
Reply | Threaded
Open this post in threaded view
|  
Report Content as Inappropriate

Re: Save Standard Tiffs

Nico Stuurman-2

On 12/21/16 10:22 AM, nranthony wrote:
> I was wondering if there's a way to save standard tiff stacks from MM?
>
> I'd love the option to save:
> rootName_ch#_timePnt#_Pos#_[etc.]_.tif
> the underscore separated increments would match the multidimensional
> acquisition I'm guessing...

Does saving as "Separate image files" (option in the MDA) do what you
want?  Otherwise, I am not quite sure what you have in mind.

Best,

Nico

------------------------------------------------------------------------------
Developer Access Program for Intel Xeon Phi Processors
Access to Intel Xeon Phi processor-based developer platforms.
With one year of Intel Parallel Studio XE.
Training and support from Colfax.
Order your platform today.http://sdm.link/intel
_______________________________________________
micro-manager-general mailing list
[hidden email]
https://lists.sourceforge.net/lists/listinfo/micro-manager-general
Reply | Threaded
Open this post in threaded view
|  
Report Content as Inappropriate

Re: Save Standard Tiffs

nranthony
Hi Nico, again, thanks for the speedy reply ;)

I think I had thought of that, but was discouraged by the individual files when z-stacks would be easier.  I need the z-stacks for import into the multi-view reconstruction plugin, but it would work for my matlab work.

Would it be possible to add z-stacks instead of individual images to MM2 NB?

Thanks
Neil
Reply | Threaded
Open this post in threaded view
|  
Report Content as Inappropriate

Re: Save Standard Tiffs

Nico Stuurman-2
On 12/21/16 1:52 PM, nranthony wrote:
> I think I had thought of that, but was discouraged by the individual files
> when z-stacks would be easier.  I need the z-stacks for import into the
> multi-view reconstruction plugin, but it would work for my matlab work.
>
> Would it be possible to add z-stacks instead of individual images to MM2 NB?

Problem is that everyone has their own favorite format and although
multiple saving formats are possible (certainly in 2.0 it should be
straight forward to add more formats), making sure that all of them work
correctly is very difficult (and making sure that data can be saved and
re-read correctly is extremely important).

If you want one z-stack per file, why not set that up in the MDA and run
your own positions, etc?  Otherwise, write a script that re-saves the
dataset in the format you like.

Best,

Nico



------------------------------------------------------------------------------
Developer Access Program for Intel Xeon Phi Processors
Access to Intel Xeon Phi processor-based developer platforms.
With one year of Intel Parallel Studio XE.
Training and support from Colfax.
Order your platform today.http://sdm.link/intel
_______________________________________________
micro-manager-general mailing list
[hidden email]
https://lists.sourceforge.net/lists/listinfo/micro-manager-general
Reply | Threaded
Open this post in threaded view
|  
Report Content as Inappropriate

Re: Save Standard Tiffs

nranthony
Hi Nico,

I understand completely, and trying to have too many options will only lead to headache.  That being said, the basic TIFF 6 standard has been around for a long time, and multi-image/multi-page tiffs are not something unusual, and as such should be re-read without troubles.  Assuming standard tags are used nearly all software can open them.

Getting back to practical current solutions, your idea of individual tiffs, plus a little code to wrap them up, will work well.

Happy holidays
Neil

Loading...