Skip to content

Classifier of Superpixels/Supervoxels

Back to MIB | User interface | Menu | Tools

Tools for automatic image segmentation using a train-and-predict scheme based on superpixel/supervoxel classification.

Overview

The Classifier of superpixels/supervoxels in Microscopy Image Browser is an effective method for automatic image segmentation, employing a train-and-predict approach. It utilizes the SLIC (Simple Linear Iterative Clustering) algorithm by Radhakrishna Achanta et al. from Ecole Polytechnique Federale de Lausanne (EPFL), Switzerland, to cluster pixels into superpixels (2D) or supervoxels (3D). These clusters are then characterized, and their features are used for classification, simplifying the segmentation process.

Dataset and the aim of the segmentation

Example dataset for cell outline segmentation

This example features a light microscopy dataset where the goal is to segment cell outlines (highlighted in green).
Due to varying cell intensities, black-and-white thresholding is ineffective, making superpixel/supervoxel classification a suitable approach.

Training the classifier

Training involves manually defining regions of interest (object and background) to build a classifier for predicting segmentation.

  • Start a new model in the Segmentation panel by clicking Create
  • Add two materials using + in the Segmentation panel
  • Rename the materials:
  • Highlight the first material, right-click, and select Rename from the context menu to name it Object
  • Rename the second material to Background similarly
Snapshot

Model setup with Object and Background materials

  • Use the Brush tool to mark areas:
  • Select cell outlines and add them to the Object material (set Add to to 1 and press A)
  • Mark background areas and add them to the Background material (set Add to to 2 and press A)
Snapshot

Manual segmentation of Object and Background

  • Launch the classifier via Menu → Tools → Classifier → Superpixel classification
  • Specify a temporary directory (default: RF_Temp next to the dataset)
Snapshot

Superpixel classifier interface

  • Configure the classifier:
  • Select mode: 2D for 2D images and superpixels, or 3D for 3D datasets and supervoxels
  • Choose superpixel type: SLIC for intensity-distinct objects, or Watershed for boundary-defined objects
  • Select Color channel for superpixel generation
  • Set Size and Compactness (for SLIC), or Size factor and Black on white (for Watershed: 0 for bright boundaries on dark background, >0 otherwise)
  • Optionally adjust the processing area using the Subarea panel
  • Click Calculate superpixels to generate superpixels
  • Click Preview superpixels to review them
Snapshot

Superpixel generation and preview

  • If superpixels are satisfactory, click Calculate features to extract features
  • Click Train & Predict to access classification settings
Snapshot

Training and prediction settings

  • In the training window:
    • Load a previous classifier with Load classifier, or train a new one if labels exist
    • Set Object to Object
    • Set Background to Background
    • Choose a classifier type in Classifier
    • Click Train classifier to start training
    • Click Predict dataset to predict segmentation
  • Check results in the Image View panel. refine by adding more markers and repeating training and prediction
Snapshot

Segmentation results

Wiping the temp directory

The classifier generates temporary files in the RF_Temp directory during prediction. Remove them by clicking Wipe Temp dir or manually delete the folder using a file explorer.

Warning

Ensure temporary files are no longer needed before wiping, as this action is irreversible

References

Back to MIB | User interface | Menu | Tools