Model Menu

Actions that can be applied to the Model layers. The Model layer is one of three main segmentation layers (Model, Selection, Mask) which can be used in combibation with other layer. See more about segmentation layers in the Data layers of Microscopy Image Browser section.

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Contents

New model

Allocates space for a new model. Use this entry when you want to start a new model or to delete the existing one. Alternatively it is possible to use the Create button in the Segmentation Panel.

Load model

Load model from the disk. By default im_browser tries to read the models in the Matlab .mat format, but it is also possible to specify other formats as well:

Note! almost any standard image format can be loaded as a model, please choose All files (_*.*) filter in the Open model dialog.

Alternatively it is possible to use the Load button in the Segmentation Panel.

Import model from Matlab

Imports model from the main Matlab workspace. Please provide a variable name from the main Matlab workspace with the model. The variable could be either a matrix with dimensions similar to those of the loaded dataset [1:height, 1:width, 1:no-slices] of the uint8 class or a structure with the following fields:

Export model to...

Exports model from MIB to other programs:

Save model

Saves model to a file in the Matlab format. The file name is not asked, which means that the im_browser will use:

Save model as...

Saves model in a number of formats:

Render model...

The segmented models can be rendered directly from MIB using one of the following methods:

The following controls are implemented:
Double click to restore the original view
Hit 'z' key over the figure to switch from ROTATION to ZOOM
    In the ZOOM mode
  • press and hold left mouse button to zoom in and out
  • press and hold middle mouse button to move the plot
Hit 'r' key over the figure to switch from ZOOM to ROTATION
    In the ROTATION mode
  • press and hold left mouse button to rotate about screen xy axis
  • press and hold middle mouse button to rotate about screen z axis
A brief demonstration is available in the following video:
https://youtu.be/dMeoIZPaDS4?t=16m56s

A demonstration is available in the following video:
https://youtu.be/DZ1Tj3Fh2HM

A demonstration is available in the following video:
Without ImarisXT https://youtu.be/MbK2JcTrZFw
With ImarisXT https://youtu.be/yODGYJUzTr0

The rendered material is specified in the Material list of the Segmentation Panel.

Fill membrane

Experimental function that should transforms lines into planar structures to make sure that the line objects on two consecutive frames overlap. This function asks for the overlap value in pixels. The function may be useful to complement the traced membranes.

Annotations...

Use this menu to modify the Annotations layer

A brief demonstration is available in the following video:
https://youtu.be/3lARjx9dPi0

Model Statistics...

Get statistics for the selected material of the model. Statistical results may be used to filter the model based on properties of its objects. The statistics dialog can also be reached from the Segmentation Panel ->Materials List->Right mouse click->Get statistics... See more here

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