CODEWITHSUNDEEP
tiffimage-segmentationimagej
rldw
rldw

Reputation: 145

How to extract parts from a 3D tiff image?

I have a tiff file that has multiple grayscale images arranged in a Z stack using ImageJ, forming a 3D image. From this image I would like to extract certain objects, i.e. cells bodies or axons.

I'm not looking for an automated segmentation, but would rather select the desired area manually. However, I wasn't able to find a software that lets me draw selections in 3D tiff images and export the selected areas.

So my question is if there is such a software?

Upvotes: 0

Views: 547

Answers (1)

Marcel
Marcel

Reputation: 522

You can use the 3D suite for that which can perfom automatic segmentations and measurements in 3D, see:

http://imagejdocu.tudor.lu/doku.php?id=plugin:stacks:3d_ij_suite:start

If you have a stack you can also manually mark and fill your objects to extract and measure them with e.g. the 3D objects counter.

Another possibility is to use the Trainable Segmentation Plugin to mark similar areas in a stack, see:

http://imagej.net/Trainable_Weka_Segmentation

Upvotes: 2

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