Tools Menu

Additional tools

Back to Index --> User Guide --> Menu


Measure length

Allows measuring the length on the image.

Measure Tool

Measure Tool of MIB is based on Image Measurement Utility written by Jan Neggers, Eindhoven Univeristy of Technology. Using this tool it is possible to perform number of different length measurements and generate intensity profiles that correspond to these measurements. Press here for details.

Line measure

Measures the linear distance between two points. Press and hold left mouse button to draw a line that connects two object. The result will be shown in the pop-up and MATLAB main window. Also the length of the measurement is copied to the system clipboard and can be pasted using the Ctrl+V key shortcut. The linear measuring tool can also be called from the toolbar. The pixel sizes are defined in the Dataset parameters.

Free hand measure

Similar to the line measure tool, except that the measured distance can be drawn arbitrarily.

Deep learning segmentation

The deep learning tool provides access to training of deep convolutional networks over the user data and utilization of those networks for image segmentation tasks.

Please refer to the corrsponding section for details: click here.


In this section MIB has two classifiers. One is designed for membrane detection but works for other objects as well. The second classifier is based on SLIC superpixels/supervoxels for the classification.

Semi-automatic segmentation

Methods for automated image segmentation and object separation.

Object separation

Tools for separation of objects that can be as materials of the current model, the mask or selection layers.

Example of seeded watersheding of cells:


The stereology tool of MIB counts number of intersections between materials of the opened model and the grid lines. The spacing between grid lines can be defined in pixels or in the image units. The results of the stereology analysis can be exported to MATLAB or Microsoft Excel.

A brief demonstration is available in the following video:

To calculate the grid use the Generate button in the Grid options panel. The analysis is started by pressing the Do stereology button.

The include annotations checkbox is selected the Stereology tool also calculates occurances of the annotation labels (Segmentation Panel->Annotations tool)

Important note! When the thickness of the grid is 1 pixel (the grid extra thickness is 0) the grid may not be shown properly at the magnifications that are lower than 100%. To see the grid also at low magnification, increase the extra grid thickness value.

Wound healing assay

The wound healing assay is designed to measure migration parameters of cells. It was tested on Imagen Cell-IQ platform that allows to obtain a grid of images taken with 0-pixel overlaps

A demonstration is available in the following video:

The tool has two parts:

  • Use the Stitching settings panel to specify number of cells in a grid; each cell defined by an own directory with images. The directory names have to be in a sequence starting from upper-left corner and progressing horizontally to the bottom-right corner
  • Specify filename extension
  • Select direcotries with the grid images for stitching (the Select directories... button)
  • Specify the output directrory for results (The Output... button)
  • Press the Stitch button to start stitching
Wound healing analysis
  • Populate the Wound healing settings panel: set the pixel size, time step and optional downsampling of resulting images for evaluation. When the show interactive graph checkbox is checked, the tool will generate an interactive plot with results after each time point
  • Select directories with the stitched images for the wound healing assay (the Select directories... button)
  • Press the Wound healing button to start
  • A plot showing minimal, average and maximal width of the wound
  • A sheet in Microsoft Excel format and a file in MATLAB format with the wound width values
  • A directory with snapshots of the detected wound
  • A text file with time stamps of the original images used during stitching
Reference The function is based on a Cell Migration in Scratch Wound Assays code provided by Constantino Carlos Reyes-Aldasoro (see more)
Cite as
CC Reyes-Aldasoro, D Biram, GM Tozer, C Kanthou Electronics Letters 44 (13), 791-793

The code is also available from github:

Back to Index --> User Guide --> Menu