VSI Reader Action Bar for ImageJ

[LAGE CRESPO Carolina RIC]

Dear all,
I have a question regarding the VSI Reader Action Bar for ImageJ.
With the current plugin, ROIs can be selected and extracted from a low-resolution thumbnail image. It would be highly useful if one could select and extract ROIs from a downscaled and better-resolved intermediate image. Would you be so kind to help me to find the best way to solve this issue?
 Two ways I can think of would be:
1) To generate a downscaled intermediate image from which to select and to extract higher resolution images;
2) To create a downscaled intermediate image used to select ROIs that are further extracted from the correspondent region in the thumbnail image. In this case, a macro that correlates the positions of the thumbnail versus the downscaled image would be highly useful.
I am not sure whether such ideas are feasible and I am very much looking forward to have your feedback.
Thank you very much in advance.
Best wishes,
Carolina Lage

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[Olivier Burri]

Dear Carolina,

Thank you for the message and apologies for the delay in my reply. This is indeed a great idea that was implemented, then scrapped then rethought and finally forgotten :)

Indeed you raise a good point. I've just finished implementing something along those lines

When you open a series for the first time using the "Select VSI" button, you get an extra menu item that prompts you which thumbnail version to use:
Tiny (by default)
Small
Medium

This is then saved to IJ.Prefs so imageJ will remember it until you change it again with another call to Select VSI. Note that this is user account-dependent.

This works very easily, but do note that currently the ROIs are dependent on the size of the thumbnail that you opened. This might change in the future, and the ROIs will be thumbnail-size independent. Just something to keep in mind for now

If you download the latest VSI reader from the update site, the new option should be available upon opening your VSI file.

Feedback is of course welcome

Best

Oli

> -----Original Message-----
> From: ImageJ Interest Group [mailto:[hidden email]] On Behalf Of
> LAGE CRESPO Carolina RIC
> Sent: Tuesday, June 9, 2015 17:52
> To: [hidden email]
> Subject: VSI Reader Action Bar for ImageJ
>
> Dear all,
> I have a question regarding the VSI Reader Action Bar for ImageJ.
> With the current plugin, ROIs can be selected and extracted from a low-
> resolution thumbnail image. It would be highly useful if one could select and
> extract ROIs from a downscaled and better-resolved intermediate image.
> Would you be so kind to help me to find the best way to solve this issue?
>  Two ways I can think of would be:
> 1) To generate a downscaled intermediate image from which to select and to
> extract higher resolution images;
> 2) To create a downscaled intermediate image used to select ROIs that are
> further extracted from the correspondent region in the thumbnail image. In
> this case, a macro that correlates the positions of the thumbnail versus the
> downscaled image would be highly useful.
> I am not sure whether such ideas are feasible and I am very much looking
> forward to have your feedback.
> Thank you very much in advance.
> Best wishes,
> Carolina Lage
>
> ________________________________
>
> [cid:imagef0dce9.JPG@25005909.4582c40d]<http://www.humanitas.it/5x100
> 0>
>
> ________________________________
>
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> ImageJ mailing list: http://imagej.nih.gov/ij/list.html

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