scale bar and profiles plotting

[Philippe GENDRE]

Deal all ImageJ list,

Some days ago I posted the following message :

-------------------------------------------------------------------------------------------------------------------------------------------------

It seems to me that the scale bar cannot be modified  and remove from an
image.

If  I am wrong please tell me how to proceed.

Another request concerns the possibility to plot several profiles (from
several ROIs) on a same plot.

I have not found how to do that.

Thanks for help

-------------------------------------------------------------------------------------------------------------------------------------------------

I have not received any answer.

I have modified RoiManager for plotting 1 to 4 line profiles on the same
plot. If anyone has some interest with that I can post the plugin.

Best regards,

Philippe

[Johannes-P. Koch]

Actually, it would Be interesting to somehow combine the scale bar and  
the overlay function in order to create a non-destructive overlay of  
the scale bar. Would that be feasible?

Best regards,
Johannes



Am 28.01.2010 um 17:33 schrieb Philippe GENDRE <[hidden email]>:

> Deal all ImageJ list,
>
> Some days ago I posted the following message :
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> ----------------------------------------------------------------------
>
> It seems to me that the scale bar cannot be modified  and remove  
> from an
> image.
>
> If  I am wrong please tell me how to proceed.
>
> Another request concerns the possibility to plot several profiles  
> (from
> several ROIs) on a same plot.
>
> I have not found how to do that.
>
> Thanks for help
>
> ---
> ---
> ---
> ---
> ---
> ---
> ---
> ---
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> ----------------------------------------------------------------------
>
> I have not received any answer.
>
> I have modified RoiManager for plotting 1 to 4 line profiles on the  
> same
> plot. If anyone has some interest with that I can post the plugin.
>
> Best regards,
>
> Philippe
>

[Glen MacDonald-2]

Dear Philippe,
Scale bars and text are drawn on the image by changing the intensities of the pixels. They cannot be saved in layers as with Photoshop.  Maybe the ObjectJ plugin will allow non-destructive annotations, if you stay within ObjectJ - I haven't used it yet . Some of the macros and plugins for annotating an image allow the user to designate placement by entering x,y offsets or drawing a rectangular ROI.  If you need to get rid of them at a later date, your options are to place annotations on a duplicate image or to place annotations in an expendable corner that can be cropped.

There was a plotting macro, maybe mentioned a few years ago, that you could perhaps modify for plotting multiple sets of values.  

Regards,
Glen
On Jan 28, 2010, at 8:33 AM, Philippe GENDRE wrote:

> Deal all ImageJ list,
>
> Some days ago I posted the following message :
>
> -------------------------------------------------------------------------------------------------------------------------------------------------
>
> It seems to me that the scale bar cannot be modified  and remove from an
> image.
>
> If  I am wrong please tell me how to proceed.
>
> Another request concerns the possibility to plot several profiles (from
> several ROIs) on a same plot.
>
> I have not found how to do that.
>
> Thanks for help
>
> -------------------------------------------------------------------------------------------------------------------------------------------------
>
> I have not received any answer.
>
> I have modified RoiManager for plotting 1 to 4 line profiles on the same
> plot. If anyone has some interest with that I can post the plugin.
>
> Best regards,
>
> Philippe

[Gabriel Landini]

On Thursday 28 January 2010, you wrote:
> Actually, it would Be interesting to somehow combine the scale bar and
> the overlay function in order to create a non-destructive overlay of
> the scale bar. Would that be feasible?

And how do you save the overlay?

G.

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

On Jan 28, 2010, at 1:00 PM, Gabriel Landini wrote:

> On Thursday 28 January 2010, you wrote:
>> Actually, it would Be interesting to somehow combine the scale
>> bar and the overlay function in order to create a non-destructive
>> overlay of the scale bar. Would that be feasible?
>
> And how do you save the overlay?

In the current version of ImageJ (1.43o), you can either save a flattened RGB version of the image, or move the selections in the overlay to the ROI Manager (Image>Overlay>To ROI Manager) and save them using More>>Save. In ImageJ 1.43p, overlays will be saved in the TIFF header. To flatten an image, press shift-f (Image>Overlay>Flatten). To add a selection to the overlay, press 'b' (Image>Overlay>Add Selection).

-wayne

[Gabriel Landini]

On Thursday 28 January 2010, you wrote:
> In the current version of ImageJ (1.43o), you can either save a flattened
>  RGB version of the image, or move the selections in the overlay to the ROI
>  Manager (Image>Overlay>To ROI Manager) and save them using More>>Save. In
>  ImageJ 1.43p, overlays will be saved in the TIFF header.

That is very useful. Can I suggest this (not sure how easy to implement it
would be): can one store any current ROIs in field tags?

I noted in the daily build that when there are overlays stored and one opens
the image these are hidden.
I though that it would be really handy to have a short string in the image
info bar, where it is shown the size and pixels, bit depth and size in bytes,
to add something like "overlays" and  "ROIs" if they are existent but hidden?

Or an option to automatically "Show overlays when opening"?

Cheers,

Gabriel

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

On Jan 30, 2010, at 4:19 AM, Gabriel Landini wrote:

> On Thursday 28 January 2010, you wrote:
>> In the current version of ImageJ (1.43o), you can either save a flattened
>> RGB version of the image, or move the selections in the overlay to the ROI
>> Manager (Image>Overlay>To ROI Manager) and save them using More>>Save. In
>> ImageJ 1.43p, overlays will be saved in the TIFF header.
>
> That is very useful. Can I suggest this (not sure how easy to implement it
> would be): can one store any current ROIs in field tags?
>
> I noted in the daily build that when there are overlays stored and one opens
> the image these are hidden.
> I though that it would be really handy to have a short string in the image
> info bar, where it is shown the size and pixels, bit depth and size in bytes,
> to add something like "overlays" and  "ROIs" if they are existent but hidden?
>
> Or an option to automatically "Show overlays when opening"?

The 1.43p daily build saves both ROIs and overlays in the TIFF header.

-wayne

[Micaela Zonta]

Dear Philippe, I've been long looking for a macro to plot several profiles
on a same plot!!!
If you could you post me the plugin I'd be very grateful!
Best regards
Micaela Zonta
PhD at Padua University
Italy

2010/1/28 Philippe GENDRE <[hidden email]>

> Deal all ImageJ list,
>
> Some days ago I posted the following message :
>
>
> -------------------------------------------------------------------------------------------------------------------------------------------------
>
> It seems to me that the scale bar cannot be modified  and remove from an
> image.
>
> If  I am wrong please tell me how to proceed.
>
> Another request concerns the possibility to plot several profiles (from
> several ROIs) on a same plot.
>
> I have not found how to do that.
>
> Thanks for help
>
>
> -------------------------------------------------------------------------------------------------------------------------------------------------
>
> I have not received any answer.
>
> I have modified RoiManager for plotting 1 to 4 line profiles on the same
> plot. If anyone has some interest with that I can post the plugin.
>
> Best regards,
>
> Philippe
>