Overlay.drawEllipse for stacks

[Guy Scott]

Hello, I have a simple question about overlaying geometric shapes. I am
using Overlay.drawEllipse to draw circles in my macro. I have my images in a
stack and I would like to draw circles at different locations for every
slice. However Overlay.drawEllipse doesn't seem to be slice specific (every
circle I draw appears in every slice of my stack). Is there a way I can
overlay geometric objects in a slice specific way?

Thanks,
Guy

[vischer]

Hello Guy,
you could try ObjectJ, which allows non-destructive marking that is aware of stack slices and hyperstacks, and bundles rois and other objects across many images into a single project file.
Look at the tab "Tutorial": it mentiones (segmented) lines and points, but also ROIs an polygons are supported.
 
- An ImageJ roi can be converted into an ObjectJ Roi via menu ObjectJ>Objects>Create Item From ROI.
- An ObjectJ ROI can be converted into an ImageJ roi via the "Object To Roi" tool.


Under the tab "Examples", there is also a worked out example "Oocytes" that includes a movie showing creation of automatic and manual non-destructive ellipses that are stack-aware.

http://simon.bio.uva.nl/objectj




> Hello, I have a simple question about overlaying geometric shapes. I am
> using Overlay.drawEllipse to draw circles in my macro. I have my images in a
> stack and I would like to draw circles at different locations for every
> slice. However Overlay.drawEllipse doesn't seem to be slice specific (every
> circle I draw appears in every slice of my stack). Is there a way I can
> overlay geometric objects in a slice specific way?
>
> Thanks,
> Guy

[Guy Scott]

Hi Norbert, thank you for your reply. This plugin does provide the
functionality I was looking for. I have encountered the following problem
using this plugin:

If I select a rectangular ROI with ImageJ and then use the Create Item from
ROI command in the ObjectJ menu, a rectangular object is created as
expected. However, when I try to use the function ojRoiToItem(); in my
macro, a 'point' object seems to be created (not a rectangular one). I have
included a .jpg file to show you what I mean:

http://img109.imageshack.us/img109/6068/objectj.jpg (the imagej ROI is still
visible in the right image)

(the left object is created using the command from the ObjectJ menu, the
second object is created by calling ojRoiToItem(); from a macro)

This is happening with a 1600x1600, 100 slice stack. Strangely, it doesn't
happen on slice 1 (both Create Item from ROI from ObjectJ menu and
ojRoiToItem() from macro produces the same object from the same rectangular
ImageJ ROI) but happens for subsequent slices.

I was having this problem using more complicated ROI which is why I decided
to try with a rectangular ROI.

Do you have any ideas what could be causing this problem?

Thanks,
Guy


On Tue, Nov 9, 2010 at 4:26 AM, Norbert Vischer <[hidden email]>wrote:

> Hello Guy,
> you could try ObjectJ, which allows non-destructive marking that is aware
> of stack slices and hyperstacks, and bundles rois and other objects across
> many images into a single project file.
> Look at the tab "Tutorial": it mentiones (segmented) lines and points, but
> also ROIs an polygons are supported.
>
> - An ImageJ roi can be converted into an ObjectJ Roi via menu
> ObjectJ>Objects>Create Item From ROI.
> - An ObjectJ ROI can be converted into an ImageJ roi via the "Object To
> Roi" tool.
>
>
> Under the tab "Examples", there is also a worked out example "Oocytes" that
> includes a movie showing creation of automatic and manual non-destructive
> ellipses that are stack-aware.
>
> http://simon.bio.uva.nl/objectj
>
>
>
>
> > Hello, I have a simple question about overlaying geometric shapes. I am
> > using Overlay.drawEllipse to draw circles in my macro. I have my images
> in a
> > stack and I would like to draw circles at different locations for every
> > slice. However Overlay.drawEllipse doesn't seem to be slice specific
> (every
> > circle I draw appears in every slice of my stack). Is there a way I can
> > overlay geometric objects in a slice specific way?
> >
> > Thanks,
> > Guy
>

[Norbert Vischer-2]

Hi Guy,

this was a bug that occured in non-z stacks, and it is fixed in ObjectJ 1.01h.
Note that when using ojRoiToItem(),  it is advisable to choose a
macro sequence like:


    ojSwitchToItem("xxx");
    ojRoiToItem();
    ojCloseObject();

regards, Norbert

On 10. Nov. 2010, at 01:27 , Guy Scott wrote:

> Hi Norbert, thank you for your reply. This plugin does provide the
> functionality I was looking for. I have encountered the following problem
> using this plugin:
>
> If I select a rectangular ROI with ImageJ and then use the Create Item from
> ROI command in the ObjectJ menu, a rectangular object is created as
> expected. However, when I try to use the function ojRoiToItem(); in my
> macro, a 'point' object seems to be created (not a rectangular one). I have
> included a .jpg file to show you what I mean:
>
> http://img109.imageshack.us/img109/6068/objectj.jpg (the imagej ROI is still
> visible in the right image)
>
> (the left object is created using the command from the ObjectJ menu, the
> second object is created by calling ojRoiToItem(); from a macro)
>
> This is happening with a 1600x1600, 100 slice stack. Strangely, it doesn't
> happen on slice 1 (both Create Item from ROI from ObjectJ menu and
> ojRoiToItem() from macro produces the same object from the same rectangular
> ImageJ ROI) but happens for subsequent slices.
>
> I was having this problem using more complicated ROI which is why I decided
> to try with a rectangular ROI.
>
> Do you have any ideas what could be causing this problem?
>
> Thanks,
> Guy
>
>
> On Tue, Nov 9, 2010 at 4:26 AM, Norbert Vischer <[hidden email]>wrote:
>
>> Hello Guy,
>> you could try ObjectJ, which allows non-destructive marking that is aware
>> of stack slices and hyperstacks, and bundles rois and other objects across
>> many images into a single project file.
>> Look at the tab "Tutorial": it mentiones (segmented) lines and points, but
>> also ROIs an polygons are supported.
>>
>> - An ImageJ roi can be converted into an ObjectJ Roi via menu
>> ObjectJ>Objects>Create Item From ROI.
>> - An ObjectJ ROI can be converted into an ImageJ roi via the "Object To
>> Roi" tool.
>>
>>
>> Under the tab "Examples", there is also a worked out example "Oocytes" that
>> includes a movie showing creation of automatic and manual non-destructive
>> ellipses that are stack-aware.
>>
>> http://simon.bio.uva.nl/objectj
>>
>>
>>
>>
>>> Hello, I have a simple question about overlaying geometric shapes. I am
>>> using Overlay.drawEllipse to draw circles in my macro. I have my images
>> in a
>>> stack and I would like to draw circles at different locations for every
>>> slice. However Overlay.drawEllipse doesn't seem to be slice specific
>> (every
>>> circle I draw appears in every slice of my stack). Is there a way I can
>>> overlay geometric objects in a slice specific way?
>>>
>>> Thanks,
>>> Guy
>>