File Menu

Provides access to some file handling actions for image dataset

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Contents

Import image from...

OMERO Import

Establish connection and load images from OMERO server. Requires OMERO server files to be downloaded. Please refer to the System Requirements pages for details of installation.

Selection of a server (please do not copy/paste the password!):

In the following dialog it is possible to select desired dataset and the range to take

A brief demonstration is available in the following video:
https://youtu.be/iR7OL0eJGuw

Batch processing...

With the batch processing mode many of the image processing operations may be designed into an image processing workflow, which may automatically applied to multiple images.

Please refer to the Batch processing... section for details.

Chopped images...

This is a special mode that allows to split a large dataset into defined number of smaller ones and combine them back later. It is also possible to fuse the previously cropped dataset to the bigger one.

Please refer to the Chopped images... section for details.

Rename and shuffle

Two tools placed under this menu entry allow to shuffle files for their blind modeling, when the user does not know which file belong to which condition. The models from the shuffled files can be converted back over the original filenames for analysis.

Please refer to the Rename and shuffle section for details.

Export image to

Export images to the main Matlab workspace or Imaris.

- Matlab
In addition to the image variable, another variable with parameters of the dataset (containers.Map class) is automatically created. This |containers.Map| can be imported back to |MIB| later together with the modified dataset to restore parameters of the dataset.

A brief demonstration on Import/Export is available in the following video:
https://youtu.be/zUJ1RUuTLVs

- Imaris
When Imaris is installed, the images can also be exported to Imaris.

Save image as

Save the open dataset to a disk. The following image formats are implemented:

Make movie

Save dataset as a movie file. All objects that are shown in the image view window will be captured. Note! If the image width is too small the scale bar is not rendered. See more here.

Make snapshot

Make snapshot of the current slice. All objects that are shown in the image view window will be captured. See more here.

Render volume

3D visualization of volumes is available using 3 different ways:

MIB rendering

Starting from MIB (version 2.5) and Matlab R2018b the volumes 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 Volume Viewer

When MIB is used with Matlab R2017a or newer it is possible to export the open dataset to Volume Viewer application. Please note that this feature is not available for the compliled version of MIB

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

Fiji 3D viewer

Please refer to details in the Microscopy Image Browser System Requirements Fiji section for installation of Fiji.

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

Additional dialog prompts for extra parameters for rendering:

Preferences

View and edit preferences of Microscopy Image Browser. Allows to modify colors of the Selection, Model and Mask layers, default behaviour of the mouse wheel and keys, settings of Undo. See more...

Please note, MIB stores its configuration parameters in a file that is automatically generated after closing of MIB:

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