Segmentation with Fiji

What is segmentation?

Partitioning a digital image into multiple segments!

Three common assumptions/requirements:

  1. Do you have overlapping objects? And do you care?

  2. What is the shape of your objects? Tubes? Blobs? Clouds?

  3. What modality was used? And how does the signal look?

Machine learning

How to segment?

1. Preprocess

Prepare your image for thresholding

2. Threshold

Separate foreground from background

3. Cleanup

Improve mask with morphological operations

4. Identify

Split foreground into objects

5. Analyze

Measure the original data

Advanced techniques:

Separating objects

Skeletonization

Spatial resolution

Uneven illumination