http://imagej.273.s1.nabble.com/newbie-needs-to-know-about-3D-tp5004118p5004121.html
which is included in Fiji. It's designed for exactly what you are
learning curve involved. It also enables automatic section series
> HOW TO MAKE A 3-D RENDERING OF OUTLINES OF NUCLEARBOUNDARIES IN AN EVENLY SPACED SET OF STAINED SECTION THROUGH A MAMMALIANBRAIN.
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> What we thought would be a reasonable approach:
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> 1. 1. Scan or photograph each section in the series,
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> 2. 2. Align the sections, ideally by reference toblockface photos taken during the sectioning process. Alterniatively, open thesections one at a time in photoshop, copying each section and placing it a alayer of a .psd file. By manipulating the images of two layers so as tonear-exactly place each layer in line with its predecessor.
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> 3. 3, Then crop the .psd file so each image frame isthe same, and the positions of the sections in the frames define the boundariesof the eventual 3D rendering.
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> 4. 4. Save each layer as a .tif file, and place all ofthem in a folder.
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> 5. 5. Drop the folder into the ImageJ window so as tomake a stack.
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> 6. 6. In each image in the stack, using the freehandtrace the outlines of the nucleus of interest.
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> HERE THE WHOLE APPROACH COLLAPSES IN CHAOS, SINCE WHEN WE TRACE ANOUTLINE ON AN IMAGE, THEN SCROLL TO THE NEXT IMAGE IN THE STACK, THE OUTLINE LEAVES THE IMAGE AND COMES WITH THESCROLL. ATTEMPTING TO DRAW ANYTHING CAUSES THE OUTLINE TO VANISH AND ONE CANNOT DRAW AN OUTLINE AROUND THE NUCLEUS IN THE NEXT IMAGE.
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> Where did we go wrong, and where can we find any instructions at allabout how to get the images and or outlines into Image J so as to continue withthe 3D rendering.?
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> Any information will be greatly appreciated,
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> John I. Johnson
>
[hidden email].
>
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