FIJI (ImageJ): Surface Plots & Rendering
ฝัง
- เผยแพร่เมื่อ 3 ก.ค. 2024
- Learn how to use FIJI (ImageJ) to create surface plots and surface render images. Different methods are introduced in this tutorial.
Timeline:
00:00 Introduction
00:10 Surface Plotter
01:26 Interactive 3D Surface Plot
05:03 SurfaceJ - surface plot rendering
06:14 Using surface plots on stacks
06:35 SurfaceJ on stacks
08:33 3D Viewer: Surface rendering
09:59 3D Viewer: Surface Plot 2D
The 3D Interactive Surface Plot can be downloaded from here:
imagej.nih.gov/ij/plugins/sur...
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Cool music btw 🤣
Hope it was more of a motivation rather than a distraction…
I personally love it :) @@johanna.m.dela-cruz
How can I quantify the %Area fraction of the surface with rough vs smooth topology based on this 3D plot?
Hello. Surface plots normally have intensity values in the 3rd dimension. Are your original images 2D or 3D? If you want to measure area fraction, you may have to threshold your images first.
@@johanna.m.dela-cruz my original image are in 2D. They are brightfield microscope image of primary skin cells with some area with stratification (higher pixel density and higher surface topology). I would like to visualize them and quantify the %area of stratification. I am not sure if surface plot and rendering is the best way to analyze my image using imageJ. Or could you kindly recommend any other methods that can achieved this goal?
There are several ways of segmenting your images so that only the stratified areas are selected for measurement. But how this can be accomplished always depends on how your images look like. Perhaps it would be best if you send me a copy of one of your images so that I could make a more specific suggestion on what you can do.
@@johanna.m.dela-cruz Amazing, thank you so much for providing help. How can I connect with you and share the image to you? Through email?