Another new project -> another corner of FIJI to come up to speed on. I think these are easy questions, which I could eventually answer by RTFM - but I’m hoping that someone here knows the answers from personal experience.
Assume a stack of gray-level images, approx. 3000x1000x300.
I think the way I want to view this stack is the standard set of 3 windows popped up by Image->Stack->Orthogonal View. I can do that, I have most of the controls mastered.
What I want to do is allow a trained observer to sketch:
a) closed polygons in the top view
b) closed polygons in the front view
c) point sets in the top view
For all of these, I want x,y,z coordinates. I’d like the coordinates in real-world dimensions. In the top view, the pixels are square (on the screen and in the real world). In the front view, the pixels are square on the screen, but not in the real world.
I know that I can (how?) specify the dimensions of a voxel in this stack. A pointer to exactly the right place would be much appreciated.
When I do that, I’m hoping that the front (and side) views will change shape so that they are geometrically correct. Right now, the front and side views are compressed on the screen (because the distance between slices, in z, is about 3-4x the distance between pixels in x and y).
My intent is to output the polygons (a and b above) and the 3D point set to a .csv file, for later processing by other programs.
Note - the polygons will all be planar, but I want the observer to be able to move up and down in the stack in between drawing polygons. So, the vertices of a given polygon in the top view will all have the same z-value, and vertices fo a given polygon in the front view will all have the same y-value. I don’t expect to need to draw anything in the side view.
Any and all hints and pointers will be most appreciated.
--
Kenneth Sloan
[hidden email] <mailto:
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Vision is the art of seeing what is invisible to others.
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