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:
- .AM, Amira Mesh - as Amira Mesh label field for models saved in Amira format
- .NRRD, Nearly Raw Raster Data - a data format compatible with 3D slicer.
- .MRC, Medical Research Council format - a data format compatible with IMOD http://bio3d.colorado.edu/imod. When using this mode, it is possible to provide a list of MRC files, where each object is encoded using its number in a separate MRC-file; after that MIB will assemble and merge all these individual objects together into a single model.
- .TIF, TIF format
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:
- .model - the field model is a matrix with dimensions similar to those of the loaded dataset [1:height, 1:width, 1:no-slices] of the uint8 class
- .materials - [_optional_] the field materials a cell array with names of the materials used in the model.
- .colors - [_optional_] a matrix with colors (0-1) for the materials of the model, [1:materialIndex, Red Green Blue]
- .labelText - [_optional_] a cell array containing labels for the annotations
- .labelPosition - [_optional_] a matrix containing positions for the annotations [1:annotationIndex, x y z]
Export model to...
Exports model from MIB to other programs:
- Matlab, export to the main Matlab workspace, as a structure (see above). The exported models may be later imported back to im_browser using the Import model from Matlab menu entry.
- Imaris as volume, export model to Imaris (if it is available, please see System Requirements section for details.
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:
- Default template such as Labels_NAME_OF_THE_DATASET.mat
- the name that was provided from the Save model as... entry
- the name that was obtained during the Load model action. The models can be saved also using the corresponding Save model button in Toolbar.
Save model as...
Saves model in a number of formats:
- .AM, Amira Mesh - as Amira Mesh label field in RAW, RAW-ASCII and RLE compressed formats. (Note! the RLE compression is very slow).
- .MAT, Matlab format - [default], Matlab native data format
- .MOD, IMOD format - contours for IMOD
- .MRC, IMOD format - volume for IMOD
- .NRRD, Nearly Raw Raster Data - a data format compatible with 3D slicer.
- .STL, STL format - triangulated mesh for use with visualization programs such as Blender.
- .TIF, TIF format
Render model...
The segmented models can be rendered directly from MIB using one of the following methods:
- Matlab isosurfaces, 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 |
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Hit 'r' key over the figure to switch from ZOOM to ROTATION |
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A brief demonstration is available in the following video: https://youtu.be/dMeoIZPaDS4?t=16m56s |
- Fiji volume..., uses 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, 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.
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
- List of annotations... - starts an auxiliary window with a list of existing annotations, see more here .
- Remove all annotations... - deletes all annotations stored with the model.
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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