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Overview

Additional tools available in MIB.

Tools Menu

Measure length

Allows measuring the length on the image.

Measure length

Measure Tool

Based on the Image Measurement Utility by Jan Neggers, Eindhoven University of Technology. Enables various length measurements and generates corresponding intensity profiles.
See Measure Tool details.

Line measure

Measures the linear distance between two points.
Press and hold to draw a line between objects.
Results will appear in a pop-up, printed to MATLAB’s main window, and copied to the clipboard (paste with Ctrl+V).
Also accessible from the Toolbar.

Note

Pixel sizes are set in Dataset parameters.

Free hand measure

Similar to line measure, but allows arbitrary drawing of the measured distance.

Deep learning segmentation

Provides training of deep convolutional networks on user data and their use for image segmentation.
See Deep Learning details.

Classifiers

Two classifiers are available in MIB.

  • Membrane detection: Uses a Random Forest classifier for automatic segmentation, based on Random Forest for Membrane Detection by Verena Kaynig and randomforest-matlab by Abhishek Jaiantilal. Works for membranes and other objects. See Random Forest help.
  • Superpixels classification: Ideal for objects with distinct intensity properties. Calculates SLIC superpixels (2D) or supervoxels (3D) and classifies them using provided labels for objects and background. See Superpixels example.

Semi-automatic segmentation

Measure length

Methods for automated image segmentation and object separation.

Graphcut and watershed example

Graphcut and Watershed

Object separation

Tools for separating objects in the current model, mask, or selection layers.
See more on object separation

Example of seeded watersheding of cells

Watershed Example

Stereology

Generate a grid and counts model materials at grid line intersections.
Results can be exported to MATLAB or Excel.
See more on about Stereology

Application of stereology to quantify surface fractions

Application of stereology to quantify surface fractions

Wound healing assay

The wound healing assay is a microscopy-based technique used to study cell migration. The Wound healing assay tool of MIB can be used to identify the wound area and measure its width.
See more about wound healing assay

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