Analysis approach for series of rodent brain section image

There are two main approaches for the analysis of rodent brain section images.

1. Pixel classification only (with two or more classes)
2. Pixel classification with two classes (immunoreactivity and background), followed by object classification with two classes (objects-of-interest and artefact).

Which approach is best for my dataset?

As a general rule, pixel classification is suitable for images in which there are clear differences in the colour, intensity and/ or texture of the feature-of-interest versus the background and other structures.  If there is non-specific labelling in the image that is very similar in appearance to the labelling-of-interest, object classification may allow the non-specific labelling to be filtered out based on object level features such as size and shape. The best approach is determined by trial and error.

Pixel classification workflow

For a quick introduction, watch: https://www.youtube.com/watch?v=5N0XYW9gRZY&feature=youtu.be

Object classification workflow