Introduction

An example workflow, covering segmentation of nuclei from a 3D image stack can be downloaded from GitHub. This example contains three files, the example workflow ("Ex1_NucleiSegmentation.mia"), the raw image stack ("Ex1_3DStack.tif") and an example of the output image that should be generated (Ex1_3DStack_S1_overlay.tif).

Each module in this workflow includes a corresponding set of notes summarising the purpose of that module and its configuration. These notes can be viewed by enabling the "Notes" panel ("View > Show notes panel" from the MIA menu) and selecting a module from the list of modules in "editing view".

While this workflow corresponds to a specific analysis, the principles covered (i.e. image loading, processing, object detection and measurements) is applicable to most workflows.

Note: The object outlines in the generated "overlay" image will only be visible when opened in ImageJ/Fiji.

Navigation

Previous: Getting started, Next: Processing view