I need to copy and crop mutiple ROI from each image

[Jasvinder Ahuja]

Dear All,
I have pictures  with three channels and 12 sections. Each picture has few
DAPI stained nuclei. I want to make a plugin that copies the in focus
section of these individual nuclei as ROI and saves it to a new location. I
have no knowledge of JAVA.

Recently, I learnt VBA. So, if you could hint me towards the right
material, I want to give it a try. Any suggestions are welcome. It would be
great if I can do this in a batch mode.

So I need info on -
How images are stored?
How to determine (algorithm) the section with the image in focus?
Can it be different sections for each channel?
Specifically how a ROI can be selected and copied?
If this can be done in a batch mode?

I am a novice. There might be information regarding the same available. It
would be great if you could point me in the right direction.

I am delighted to see how this forum works. And would appreciate any
inputs/help

Jasvinder
Boerner Lab
Cleveland State University

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[Pariksheet Nanda]

On Mon, Oct 22, 2012 at 11:08 AM, Jasvinder Ahuja
<[hidden email]> wrote:
> I want to make a plugin that copies the in focus section of these individual
> nuclei as ROI and saves it to a new location.
>

Can you explain in a little more detail why you want to do this?
What is the information you want to extract from your multi-channel Z series?

If you want a better view of in focus sections of the image, you could use:
    Image > Stacks > Z Project...
Although this command is in the Stacks menu, it will also work on your
Hyperstack.
Then, to see multiple channels at once you can use the contrast tools from:
   Image > Color > Channels Tool
...and use "Composite" and check the channels you want.
Lastly to limit the Lookup Table (LUT) to in-focus fluorescence you can use:
    Image > Adjust > Brightness/Contrast...
...and adjust the minimum threshold (first slider)


> I have no knowledge of JAVA.  Recently, I learnt VBA.
--snip--
> It would be great if I can do this in a batch mode.
>

I don't yet see that you have a need for programming in ImageJ.
If you wanted to, you should start with the Macro programming ability:
http://imagej.nih.gov/ij/developer/index.html
The top link "Macro Language" describes this in some detail.
The Macro Language is similar to JavaScript, but does not have many of
JavaScript's other features like objects and instead relies on
declaring functions outside of the macro for reusable code.


> Jasvinder
>

Pariksheet

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[Jasvinder S Ahuja]

Thanks Pariksheet fot the detailed response, I appreciate it. I have two problems still -
1) I cannot save the ROI as an image (.tiff file) On average I have 5-10 ROI per image. I want to save each ROI as an image in a format easy for ImageJ to handle.

2) Also I am having problems opening deconvolved image files from deltavision (*R3D_D3D.dv). Deltavision_opener plugin opens the non deconvolved file (*R3D.dv). I believe this should be a simple fix but have no clue, on how to go about it.

Thanks Again,r
Jasvinder

[Pariksheet Nanda]

On Sunday, December 9, 2012, Jasvinder S Ahuja wrote:
>
> 1) I cannot save the ROI as an image (.tiff file) On average I have 5-10
> ROI
> per image.


Add your ROIs to the ROI manager. There are two ways to save the ROI
information:
- save to .roi file from the manager
http://rsbweb.nih.gov/ij/docs/menus/analyze.html#manager
- if you just save the .tiff image it should include the ROI drawn on the
image as well, so you will see the ROI the next time you open it in ImageJ.



> I want to save each ROI as an image in a format easy for ImageJ
> to handle.
>

Using the .roi file explained above will accomplish this.


2) Also I am having problems opening deconvolved image files from
> deltavision (*R3D_D3D.dv). Deltavision_opener plugin opens the non
> deconvolved file (*R3D.dv). I believe this should be a simple fix but have
> no clue, on how to go about it.
>

 I don't see support for that file with the LOI Bioformats plugin[1] so
another approach could be to import the raw DeltaVision data into ImageJ
and run deconvolution in ImageJ instead, or have DeltaVision export to a
format ImageJ understands.


Jasvinder
>

 Pariksheet

[1] http://loci.wisc.edu/bio-formats/formats

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[Dubuis, Eric D]

To the question: How to save my ROI as image ?

If what you want is just an illustration of the ROI used, you can always copy system them while they are superimposed to your image (Alt Gr + Print Screen).

Alternatively, transform your tiff image to RGB, display your ROI on screen then in ROI manager window use the command Flatten (F), This will merge your ROI to the RGB image which you can later save as Tiff. I advise to have a thicker line to mark the edge of thr ROI si it is visible on the merged picture

If all you want to get is your ROI on a transparent background, open your image, im the menu select:
Image -> Stacks -> Add Slice
Give the new slice a black background and display your ROI (again, thick line for the edges). Use Flatten (F) command and answer "No" when the software ask if you want to flatten all images. You will get your ROI on a black background. Save that image (either as jpg, bmp or other).
Use an imaging software (photoshop or the gimp for example) and open the image. Using color select (or magic wand like method) select and remove all black from the picture so as to see your ROI without background. Save the image as png.
Later when inserting it into power point or in web pages, you will have your ROI on transparent background which you will be able to superimpose to whatever you want.

Cheers


-----Original Message-----
From: ImageJ Interest Group [mailto:[hidden email]] On Behalf Of Pariksheet Nanda
Sent: 13 December 2012 13:36
To: [hidden email]
Subject: Re: I need to copy and crop mutiple ROI from each image

On Sunday, December 9, 2012, Jasvinder S Ahuja wrote:
>
> 1) I cannot save the ROI as an image (.tiff file) On average I have
> 5-10 ROI per image.


Add your ROIs to the ROI manager. There are two ways to save the ROI
information:
- save to .roi file from the manager
http://rsbweb.nih.gov/ij/docs/menus/analyze.html#manager
- if you just save the .tiff image it should include the ROI drawn on the
image as well, so you will see the ROI the next time you open it in ImageJ.



> I want to save each ROI as an image in a format easy for ImageJ
> to handle.
>

Using the .roi file explained above will accomplish this.


2) Also I am having problems opening deconvolved image files from
> deltavision (*R3D_D3D.dv). Deltavision_opener plugin opens the non
> deconvolved file (*R3D.dv). I believe this should be a simple fix but have
> no clue, on how to go about it.
>

 I don't see support for that file with the LOI Bioformats plugin[1] so
another approach could be to import the raw DeltaVision data into ImageJ
and run deconvolution in ImageJ instead, or have DeltaVision export to a
format ImageJ understands.


Jasvinder
>

 Pariksheet

[1] http://loci.wisc.edu/bio-formats/formats

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[Melissa Linkert-2]

Hi,

> 2) Also I am having problems opening deconvolved image files from
> > deltavision (*R3D_D3D.dv). Deltavision_opener plugin opens the non
> > deconvolved file (*R3D.dv). I believe this should be a simple fix but have
> > no clue, on how to go about it.
> >
>
>  I don't see support for that file with the LOI Bioformats plugin[1] so
> another approach could be to import the raw DeltaVision data into ImageJ
> and run deconvolution in ImageJ instead, or have DeltaVision export to a
> format ImageJ understands.

Please note that Deltavision (*.dv) files are supported by Bio-Formats:

https://www.openmicroscopy.org/site/support/bio-formats/formats/deltavision.html

Regards,
-Melissa

On Thu, Dec 13, 2012 at 08:36:20AM -0500, Pariksheet Nanda wrote:

> On Sunday, December 9, 2012, Jasvinder S Ahuja wrote:
> >
> > 1) I cannot save the ROI as an image (.tiff file) On average I have 5-10
> > ROI
> > per image.
>
>
> Add your ROIs to the ROI manager. There are two ways to save the ROI
> information:
> - save to .roi file from the manager
> http://rsbweb.nih.gov/ij/docs/menus/analyze.html#manager
> - if you just save the .tiff image it should include the ROI drawn on the
> image as well, so you will see the ROI the next time you open it in ImageJ.
>
>
>
> > I want to save each ROI as an image in a format easy for ImageJ
> > to handle.
> >
>
> Using the .roi file explained above will accomplish this.
>
>
> 2) Also I am having problems opening deconvolved image files from
> > deltavision (*R3D_D3D.dv). Deltavision_opener plugin opens the non
> > deconvolved file (*R3D.dv). I believe this should be a simple fix but have
> > no clue, on how to go about it.
> >
>
>  I don't see support for that file with the LOI Bioformats plugin[1] so
> another approach could be to import the raw DeltaVision data into ImageJ
> and run deconvolution in ImageJ instead, or have DeltaVision export to a
> format ImageJ understands.
>
>
> Jasvinder
> >
>
>  Pariksheet
>
> [1] http://loci.wisc.edu/bio-formats/formats
>
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> ImageJ mailing list: http://imagej.nih.gov/ij/list.html

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[Jasvinder S Ahuja]

Hey Pariksheet,

Thanks. To save all ROI with slices I used -

      roiManager("select", 0); 

      roiManager("Remove Slice Info");

      run("Duplicate...", "title=myID duplicate channels=1-3 slices 1-14"); 

And modified the deltavision_opener to work with deconvolved images.

It works great now.

Thanks

Jasvinder

On Thu, Dec 13, 2012 at 8:37 AM, Pariksheet Nanda [via ImageJ] <[hidden email]> wrote:

On Sunday, December 9, 2012, Jasvinder S Ahuja wrote:
>
> 1) I cannot save the ROI as an image (.tiff file) On average I have 5-10
> ROI
> per image.

Add your ROIs to the ROI manager. There are two ways to save the ROI
information:
- save to .roi file from the manager
http://rsbweb.nih.gov/ij/docs/menus/analyze.html#manager
- if you just save the .tiff image it should include the ROI drawn on the
image as well, so you will see the ROI the next time you open it in ImageJ.

> I want to save each ROI as an image in a format easy for ImageJ
> to handle.
>

Using the .roi file explained above will accomplish this.

2) Also I am having problems opening deconvolved image files from
> deltavision (*R3D_D3D.dv). Deltavision_opener plugin opens the non
> deconvolved file (*R3D.dv). I believe this should be a simple fix but have
> no clue, on how to go about it.
>

 I don't see support for that file with the LOI Bioformats plugin[1] so
another approach could be to import the raw DeltaVision data into ImageJ
and run deconvolution in ImageJ instead, or have DeltaVision export to a
format ImageJ understands.


Jasvinder
>

 Pariksheet

[1] http://loci.wisc.edu/bio-formats/formats

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[Jasvinder S Ahuja]

Thanks, for the nice suggestions!

On Thu, Dec 13, 2012 at 8:53 AM, Dubuis, Eric D <[hidden email]>wrote:

> To the question: How to save my ROI as image ?
>
> If what you want is just an illustration of the ROI used, you can always
> copy system them while they are superimposed to your image (Alt Gr + Print
> Screen).
>
> Alternatively, transform your tiff image to RGB, display your ROI on
> screen then in ROI manager window use the command Flatten (F), This will
> merge your ROI to the RGB image which you can later save as Tiff. I advise
> to have a thicker line to mark the edge of thr ROI si it is visible on the
> merged picture
>
> If all you want to get is your ROI on a transparent background, open your
> image, im the menu select:
> Image -> Stacks -> Add Slice
> Give the new slice a black background and display your ROI (again, thick
> line for the edges). Use Flatten (F) command and answer "No" when the
> software ask if you want to flatten all images. You will get your ROI on a
> black background. Save that image (either as jpg, bmp or other).
> Use an imaging software (photoshop or the gimp for example) and open the
> image. Using color select (or magic wand like method) select and remove all
> black from the picture so as to see your ROI without background. Save the
> image as png.
> Later when inserting it into power point or in web pages, you will have
> your ROI on transparent background which you will be able to superimpose to
> whatever you want.
>
> Cheers
>
>
> -----Original Message-----
> From: ImageJ Interest Group [mailto:[hidden email]] On Behalf Of
> Pariksheet Nanda
> Sent: 13 December 2012 13:36
> To: [hidden email]
> Subject: Re: I need to copy and crop mutiple ROI from each image
>
> On Sunday, December 9, 2012, Jasvinder S Ahuja wrote:
> >
> > 1) I cannot save the ROI as an image (.tiff file) On average I have
> > 5-10 ROI per image.
>
>
> Add your ROIs to the ROI manager. There are two ways to save the ROI
> information:
> - save to .roi file from the manager
> http://rsbweb.nih.gov/ij/docs/menus/analyze.html#manager
> - if you just save the .tiff image it should include the ROI drawn on the
> image as well, so you will see the ROI the next time you open it in ImageJ.
>
>
>
> > I want to save each ROI as an image in a format easy for ImageJ
> > to handle.
> >
>
> Using the .roi file explained above will accomplish this.
>
>
> 2) Also I am having problems opening deconvolved image files from
> > deltavision (*R3D_D3D.dv). Deltavision_opener plugin opens the non
> > deconvolved file (*R3D.dv). I believe this should be a simple fix but
> have
> > no clue, on how to go about it.
> >
>
>  I don't see support for that file with the LOI Bioformats plugin[1] so
> another approach could be to import the raw DeltaVision data into ImageJ
> and run deconvolution in ImageJ instead, or have DeltaVision export to a
> format ImageJ understands.
>
>
> Jasvinder
> >
>
>  Pariksheet
>
> [1] http://loci.wisc.edu/bio-formats/formats
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>

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[Antoinette]

I consider the image cropping as one of the fundamental functions of an image process project. As I use vb to program, I would like to share my image cropping method here:

Public Shared Function ApplyCrop(img As REImage, x As Integer, y As Integer, width As Integer, height As Integer) As Integer

[Antoinette]

I consider the image cropping as one of the fundamental functions of an image process project. As I use vb to program, I would like to share my image cropping method here:

Public Shared Function ApplyCrop(img As REImage, x As Integer, y As Integer, width As Integer, height As Integer) As Integer