Remove Background

[kavanaa1]

Hi,

I've a couple thousand JPEG image slices of metal samples - I want to remove the black background from the slices so when I view in 3D viewer I am just seeting the specimen. How can I do this in Image J? Threshold manager doesnt seem to be working for me, the way I am using it.

Thanks

[Krs5]

As far as I can see you should be able to view your specimen in the 3D viewer without changes to the background

Kees

________________________________________
From: ImageJ Interest Group [[hidden email]] on behalf of kavanaa1 [[hidden email]]
Sent: 14 May 2016 15:51
To: [hidden email]
Subject: Remove Background

<http://imagej.1557.x6.nabble.com/file/n5016440/sample_a3_axial_0270.jpg> Hi,

I've a couple thousand JPEG image slices of metal samples - I want to remove
the black background from the slices so when I view in 3D viewer I am just
seeting the specimen. How can I do this in Image J? Threshold manager doesnt
seem to be working for me, the way I am using it.

Thanks





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[kavanaa1]

I can use 3D viewer but the specimen is on the centre of the black box (i.e the background) so it's not possible to see the outer surface of the specimen. I did try put a circular  selection area around he specimen and use the Remove Outside crop feature. This works but I lose the outer specimen surface entirely. I am looking to remove the background but retain the specimen info of possible 

Thanks for your reply 

Alan

On Saturday, 14 May 2016, Straatman, Kees (Dr.) [via ImageJ] <[hidden email]> wrote:

As far as I can see you should be able to view your specimen in the 3D viewer without changes to the background

Kees

________________________________________
From: ImageJ Interest Group [[hidden email]] on behalf of kavanaa1 [[hidden email]]
Sent: 14 May 2016 15:51
To: [hidden email]
Subject: Remove Background

<http://imagej.1557.x6.nabble.com/file/n5016440/sample_a3_axial_0270.jpg> Hi,

I've a couple thousand JPEG image slices of metal samples - I want to remove
the black background from the slices so when I view in 3D viewer I am just
seeting the specimen. How can I do this in Image J? Threshold manager doesnt
seem to be working for me, the way I am using it.

Thanks





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[Joel Sheffield]

It seems to me that the 3D viewer has a transparency option that might help
you.  An alternative possibility is to reverse the color map on your images
so that the black background appears white.  Would it be possible to post
one of your image sets so that we could experiment with it?

Joel



Joel B. Sheffield, Ph.D
Department of Biology
Temple University
Philadelphia, PA 19122
Voice: 215 204 8839
e-mail: [hidden email]
URL:  *http://tinyurl.com/khbouft <http://tinyurl.com/khbouft>*

On Sat, May 14, 2016 at 10:51 AM, kavanaa1 <[hidden email]> wrote:

> <http://imagej.1557.x6.nabble.com/file/n5016440/sample_a3_axial_0270.jpg>
> Hi,
>
> I've a couple thousand JPEG image slices of metal samples - I want to
> remove
> the black background from the slices so when I view in 3D viewer I am just
> seeting the specimen. How can I do this in Image J? Threshold manager
> doesnt
> seem to be working for me, the way I am using it.
>
> Thanks
>
>
>
>
>
> --
> View this message in context:
> http://imagej.1557.x6.nabble.com/Remove-Background-tp5016440.html
> Sent from the ImageJ mailing list archive at Nabble.com.
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>

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[Krs5]

Dear Alan,

Attached is the image you supplied in the original email directly viewed in the 3D viewer. Do you have the latest version of ImageJ/Fiji and of the 3D viewer?

Kees

-----Original Message-----
From: ImageJ Interest Group [mailto:[hidden email]] On Behalf Of kavanaa1
Sent: 14 May 2016 17:29
To: [hidden email]
Subject: Re: Remove Background

I can use 3D viewer but the specimen is on the centre of the black box (i.e the background) so it's not possible to see the outer surface of the specimen. I did try put a circular  selection area around he specimen and use the Remove Outside crop feature. This works but I lose the outer specimen surface entirely. I am looking to remove the background but retain the specimen info of possible

Thanks for your reply

Alan

On Saturday, 14 May 2016, Straatman, Kees (Dr.) [via ImageJ] <
[hidden email]> wrote:

> As far as I can see you should be able to view your specimen in the 3D
> viewer without changes to the background
>
> Kees
>
> ________________________________________
> From: ImageJ Interest Group [[hidden email]
> <http:///user/SendEmail.jtp?type=node&node=5016441&i=0>] on behalf of
> kavanaa1 [[hidden email]
> <http:///user/SendEmail.jtp?type=node&node=5016441&i=1>]
> Sent: 14 May 2016 15:51
> To: [hidden email]
> <http:///user/SendEmail.jtp?type=node&node=5016441&i=2>
> Subject: Remove Background
>
> <http://imagej.1557.x6.nabble.com/file/n5016440/sample_a3_axial_0270.j
> pg>
> Hi,
>
> I've a couple thousand JPEG image slices of metal samples - I want to
> remove the black background from the slices so when I view in 3D
> viewer I am just seeting the specimen. How can I do this in Image J?
> Threshold manager doesnt seem to be working for me, the way I am using
> it.
>
> Thanks
>
>
>
>
>
> --
> View this message in context:
> http://imagej.1557.x6.nabble.com/Remove-Background-tp5016440.html
> Sent from the ImageJ mailing list archive at Nabble.com.
>
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> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
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[kavanaa1]

Hi Joel

The 3D Viewer transparency option does work you are right. However if I want to do use the Volume Viewer or Volume Est plugins for example they really work with the black background. If you can try the color map reversal please feel do, I'd be eager to see how it works. I dont know how to bulk upload several files so I've just individually uploaded some slices that hopefully you can use for this.

Thanks for your help / time

cropped_cropped_Sample_A30572.tifcropped_cropped_Sample_A30573.tifcropped_cropped_Sample_A30574.tifcropped_cropped_Sample_A30575.tifcropped_cropped_Sample_A30576.tifcropped_cropped_Sample_A30577.tif