Tools Ribbon Tab¶

Overview¶

Additional tools available in MIB.

Segmentation Section¶

Deep learning segmentation¶

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

See Deep Learning details.

Classifiers¶

Pixel classification methods for automated segmentation.

Membrane detector¶

Uses a Random Forest classifier for automatic segmentation based on membrane or other object appearance.

Based on Random Forest for Membrane Detection by Verena Kaynig and randomforest-matlab by Abhishek Jaiantilal.

See Random Forest help.

Semi-automatic segmentation¶

Methods for automated image segmentation.

Global thresholding¶

Segments objects by intensity threshold applied across the whole dataset.

See Global thresholding details.

Graphcut¶

Graph-cut based segmentation — robust for objects with overlapping intensity distributions.

See Graphcut segmentation details.

Misc Section¶

Measure tool¶

Interactive measurement tools for distances and intensity profiles.

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 appear in a pop-up, printed to MATLAB's main window, and copied to the clipboard (paste with Ctrl+V).

Also accessible from the Quick Access Bar.

Free hand measure¶

Similar to line measure, but allows drawing an arbitrary path for the measured distance.

Object separation¶

Tools for separating touching or overlapping objects in the current model, mask, or selection layers.

See Object separation details.

Stereology¶

Generates a grid and counts model materials at grid-line intersections. Results can be exported to MATLAB or Excel.

See Stereology details.

Wound healing assay¶

The wound healing assay is a microscopy-based technique used to study cell migration. This tool identifies the wound area and measures its width.

See Wound healing assay details.

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