After taking microscopic images under a confocal microscope you can compiled all the optical sections in the form of a 3D image. I need to do this for a few of the stacks (sections) by taking advantage of Image J software.
Hi Mohammad,
a simple built-in way is to make a 3D projection movie. This is under "Image > Stacks > 3D Project". There are also a bunch of Plugins which make surface views. One is built in under Plugins > 3D. This is the 3D viewer. There is also the Volume Viewer, which you have to download from the ImageJ Plugins website. (might be built in in newer versions of ImageJ)
Does that answer your question?
Hi Mohammad,
If you want to render your stack and visualize in 3D, then Fiji has the convenience that it comes with the 3D Viewer plugin installed under ImageJ. Follow these steps in Fiji:
- activate your stack (click on it)
- go to Plugins/3D Viewer
- accept the default settings
The volume-rendered image must appear in a new window, you can rotate it by left mouse click. You need a reasonably recent and powerful graphics card and RAM, depending on the XY size and slice number of your stack(s).
Regards,
Janos
--
Janos Kriston-Vizi, PhD
Group Leader of Bioinformatics Image Core (BIONIC)
Medical Research Council. Laboratory for Molecular Cell Biology
University College London. Gower Street, WC1E 6BT London, UK
Mohammad,
I agree with Janos' answer. Use the 3D viewer plugin for ImageJ. It is included with Fiji, but can be added manually to ImageJ. You can create volume renders, surfaces, orthoslices, time-lapse movies, animated rotations and more.
Good luck
1. Import > Image sequence> \\select the file in the folder>open>\\set sequence options>OK
2. Image> 3D viewer> \\change properties in Add> OK
Now the 2D images will be compiled to form a 3D one. You can conveniently do operations like zoom, rotate, slice, etc.
If you have 2 colours, 2 channels, in the same file all the stacks, how you merge it to perform a 3D inahe wirh green and red colours?
ImageJ / Fiji allows you to arbitrarily assign any channel to any colour, making each focal plane either a composite or an RGB image. Use Image>Colour>Merge Channels or Image>Colour>Arrange Channels.
Yes I make it Bryan but I have only success one 1 image red and 1 image green. I made the merge. the sitacuon is when you have an stack file in whcih images 1-10 are red (protein X) and imagees 11-18 are mitochondria in green por example...i could not reconstruct a merge 3D
hello
i have 80 slice of 2D image
so can i make a 3D image of this slices by this software????
Hi Agustina,
Sorry for being so slow to get back to you, I didn't see that you had followed up.
You can split your stack into two substacks, and then use the colour merge tool to put one stack into one channel and the other stack into another channel, such that you have a multicolour stack showing both datasets in 3D. So for your example with channel 1 in focal planes 1-10, and channel 2 in focal planes 11-18, you'd do something like this:
Image>Stacks>Tools>Make Substack, select 1-10 and create a new stack called "Protein X", then Image>Stack>Tools>Make Substack, select 11-18 and create a new stack called "Mitochondria".
Then you want to merge your stack using the Image>Colour>Merge tool, but to do that, you need both stacks to have the same number of focal planes. So you'd have to add a couple of focal planes to the "Mitocondria" stack to get 10 focal planes using Image>Stacks>AddSlice.
Once you've got two stacks with the same dimensions, you can just use Image>Colour>Merge Channels to put one stack in Cyan and one in Magenta, or or whatever other combination of colours you want.
And Zhara,
Image>Stacks>Images to Stack does what you want.
Cheers
In my 3D image, there are 2 mice limbs. When i did CT scan i put the limbs side by side, but scanned together. How do i can separate, i need to measure the length of tibia and femur.
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