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I have 100 tif images from confocal microsocpy that have black background (NOT alpha) and I would like to stack them to recreate some color labeled structures in 3D. In order to do that, I need to make the black color transparent. I tried to mix diffuse and transparent shaders, but I don't really know how to indicate the black color to be transparent.

confocal microscopy plane

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Yes.

First Cycles Texture Non Color then Mix Transparency and Emission.

enter image description here

Nodes

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You might consider processing your images once as format .png for you later convenience and node convenience.

Second a sample from Blender Render. UV Mapped Image. Texture 01 Image .. calculate transparency. Threshold with color ramp gray scale . Affect color and transparency. Texture 02 color only multiply. You may want to threshold because the image may not be black exactly where you might first think. There are many was to do this. Torus Background and Text to show transparency.

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2 Textures. Note the color ramp. enter image description here

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  • $\begingroup$ You are welcome. That's how business should occur here. Clear question and acceptable answer . Answer marked as acceptable quickly. All in about 3 hours. Keep in mind we might be edited because we said ... Thank You and Welcome. $\endgroup$ – atomicbezierslinger Oct 3 '14 at 17:43
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    $\begingroup$ Just curious.. What is that arrow supposed to be? $\endgroup$ – gandalf3 Oct 3 '14 at 18:06
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    $\begingroup$ @atomicbezierslinger It is true that questions and answers will be edited to remove thanks, etc. but that is what the comments are for. Nice answer. $\endgroup$ – David Oct 4 '14 at 2:22
  • $\begingroup$ i must know how you made that arrow. $\endgroup$ – Joseph Farah Nov 10 '16 at 23:08
  • $\begingroup$ @JosephFarah . The arrow was made in A donotbe Illustrator. Wait, maybe it was childish a creation in Blender 3D Cycles, for inquiries more so. It is the equivalent of a horse hair shirt worn in reverse, haunting me every waking moment. A tangled mass of thorny vines onto which I have fallen adorsed without protection. It was also meant to be swollen and grotesque. Oh yes, visible. How odd I had the urge open a new web page with Blender as the starting point. $\endgroup$ – atomicbezierslinger Nov 12 '16 at 20:44
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I found using the color key node, selecting the color black for the color, and playing around the H, S, V numbers till I wanted to work nicely for getting the color black, then making the background transparent in the settings

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