Display 3D pseudocolor images with threhshold and transparency adjustment

[homedoc]

Hello to all,

We have a 3D stack of grayscale images. We would like to:
(1) Apply a LUT;
(2) Convert the resulting color display to either real RGB or real pseudocolor images; and
(3) Final goal: Display trhe result in color with variable transparency and threshold using the ImageJ 3D Viewer or perhaps another similar plug-in if one is available.

Any suggestions on how to achieve (3) will be greatly appreciated.

Thanks in advance,
Dr. Dave Tulbert  

[Nathaniel Ryckman]

I'm kind of confused at what the problem is. It sounds like you have a pretty good plan already?

Here is a Youtube video explaining how to use the 3D displayer:

http://www.youtube.com/watch?v=cD3Hc3NYkaU

If it doesn't help, could you try to explain the dilemma a little more? Examples would also help.

homedoc wrote

Hello to all,

We have a 3D stack of grayscale images. We would like to:
(1) Apply a LUT;
(2) Convert the resulting color display to either real RGB or real pseudocolor images; and
(3) Final goal: Display trhe result in color with variable transparency and threshold using the ImageJ 3D Viewer or perhaps another similar plug-in if one is available.

Any suggestions on how to achieve (3) will be greatly appreciated.

Thanks in advance,
Dr. Dave Tulbert

[homedoc]

Thanks for the input Nathaniel.

I was able to colorize the gray scale data by converting it to 8 bit, then applying a LUT, then converting it to 24 bit RGB and finally using Image/Color/Merge channels. Then I can display it as a 3D volume.

The only remaining problem is that the transparency function in the 3D viewer really does not work as it should (i.e. as an alpha channel). That is, you cannot see the inner layers of the volume through the outer layers of the volume. Does ImageJ have a plug-in that supports true transparency rendering through a 32 bit RGB image where 8 bits is an alpha value, or some other mechanism?

Dave Tulbert

[Chiz]

Hi Dave,

I just had a similar problem; here is what I found out.

Assuming you have 16 bit gray scale stack.

>>(1) Apply a LUT;

Image -> Lookup Tables -> choose a LUT of your choice.


>>(2) Convert the resulting color display to either real RGB or real pseudocolor images; and

Image -> Type -> RGB Color.


>>(3) Final goal: Display trhe result in color with variable transparency and threshold using the ImageJ 3D Viewer or perhaps another similar plug-in if one is available.

Plugins -> 3D -> 3D Viewer. Choose your image stack. Make sure you select "None" for Color.

Then you click on your 3D object; a red bounding box should appear. Go to 3D Viewer's Menu -> Edit -> Attributes -> Adjust threshold or Change transparency.

Good luck,

Ippei Kotera

[homedoc]

Thanks Ippei,

Here is a series of screen dumps embedded in a PDF. The sequence of images plus their embedded comments illustrates the transparency issue clearly.

The image stack was created as follows:

(1) Import a RAW file containing 18 slices of 648 x 482 gray scale images (64 bit floating point).

(2) Adjust Brightness-contrast by setting maximum intensity 700 to normalize display and show complete intensity range.

(3) Convert stack to 8 bit. (Image properties then verifies that image range is 0 - 255)

(4) Increase size of stack from 18 slices to 360 slices.

(5) Apply LUT ("Fire")

(6) Convert stack to 24 bit RGB.

(7) Create orthoslice and volume displays using Plugins/3D/3D viewer.

Best regards to all,

Dave Tulberttransparency_issue_s.pdf