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

Type of the model

Display type of the current model:

Work with models with more than 255 materials

Materials should be named with numbers that represent the index of the current working material. For example, in the image below the current working material for the brush tool is 11555.

Selection of material for work can be done either by the right mouse click over the segmentation table and seletion of the Rename... entry in the menu; or by moving the mouse over the desired object in the Image View panel and press the Ctrl + F shortcut.

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 MIB tries to read the models in the Matlab format (.model), 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 MIB 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:

MIB rendering

Starting from MIB (version 2.5) and Matlab R2018b the materials can be directly visualized in MIB using hardware accelerated volume rendering engine. The datasets for visuzalization can be downsampled during the export. It is possible to make snapshots and animations.

Limitations:

A brief demonstration is available in the following video:
https://youtu.be/J70V33f7bas

Matlab isosurface

MIB uses Matlab engine to generate isosurfaces from the models and visualize those using a modification of the view3d function written by Torsten Vogel.

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 videos:
https://youtu.be/svAFGBRfeoI
https://youtu.be/dMeoIZPaDS4?t=16m56s

Matlab isosurface and export to Imaris

MIB uses Matlab engine to generate isosurfaces from the models and export the resulting surfaces to Imaris for visualization.

A demonstration is available in the following video:
https://youtu.be/nDpC8b8lqo4

Matlab volume viewer

Matlab volume viewer, render the model using Matlab volume viewer, available only for the Matlab version of MIB and requires R2017b - R2019b or newer. For the release R2019b, the materials may be displayed together with the volume, but there are not control for lightning, so it is not very convenient.

Demonstration of the visualization of models as Volumes:
https://www.youtube.com/watch?v=J70V33f7bas
Demonstration of the visualization of models as materials together with the image dataset:
https://youtu.be/GM9V1IxNkTI

Fiji volume

MIB can use Fiji 3D viewer for visualization of the model as a volume (click here for details. (requires Fiji to be installed, see here).

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

Imaris surface

Imaris surface, render the model in Imaris; requires Imaris and ImarisXT to be installed, see here

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.

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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