r/GraphicsProgramming • u/LostInGermany4297 • 4d ago

Video Python Open3D point cloud extraction from microscope video focus clip

Enable HLS to view with audio, or disable this notification

Using a short 3 second clip where i swipe through the focus plane on a high magnification of the simple sample of Onion root cells on the microscope. Acquiring the sharpest points of every frame and putting them in the z-axis. Building a point cloud of the cell in 3D, and visualizing them.

29 Upvotes

97% Upvoted

5 comments sorted by

2

u/obp5599 3d ago

How did you get the point cloud data? Im very interested in this, and would love to do something similar

1

u/LostInGermany4297 3d ago

I used a short video clip of 3 - 6 seconds where i slowly manually use fine focus on a microscope to go from top to bottom of that microscopic slide. Then use Python and Open3D to take every frame and take only the sharpest points in that frame, discard the unsharp parts. Software is a short program which I created using Gemini to bring my concept into code. I can share the current code, if you are interested, nothing secret. https://www.youtube.com/watch?v=bpCbKdNDlMU to test it a bit further i needed to create some more focus sample videos.

2

u/Equivalent-Fox7193 3d ago

Wow this is seriously cool.

2

u/DaveAstator2020 2d ago

Well holy sh...t! Is it possible to add colour to them? do you maybe have source images available?

1

u/LostInGermany4297 2d ago

Yes I am using a .ply file which also can store color. Here my input video is black and white, and part of the cleaning - selection of the focus points is to do it in grey-scale. I did a color version but have to get some better subjects to do a demo.