File Menu
Provides access to some file handling actions for image dataset
Back to Index --> User Guide --> Menu
Contents
Import image from...
- Matlab imports image from the main Matlab workspace into im_browser. It is possible to provide image description containers.Map together with the dataset, which allows to maintain parameters of the dataset when using the Export image command (see below). [*brief demo*]
- Clipboard pastes image from the system clipboard. This functionality is implemented using IMCLIPBOARD function by Jiro Doke, MathWorks, 2010. [*brief demo*]
- Imaris imports dataset from Imaris; requires Imaris and ImarisXT. This functionality is done with IceImarisConnector written by Aaron C. Ponti, ETH Zurich. [*demo*]
- URL opens image from provided URL address. The link should contain the protocol type (e.g., http://). [*brief demo*]
OMERO Import
Establishes connection and loads 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:
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
Chopped images...
This is a special mode that allows to chop and combine back the opened dataset to a defined number of smaller volumes.
Please refer to the Chopped images... section for details.
Export image to Matlab
Export images to the main Matlab workspace. 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 im_browser 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
Save image as
Saves the dataset to a disk. The following image formats are implemented:
- AM, Amira Mesh - as Amira Mesh binary format
- JPEG, Joint Photographic Experts Group - a method for saving lossy compressed RGB datasets
- HDF5, Hierarchical Data Format - saves images in the Hierarchical Data Format, version 5
- MRC, MRC format for IMOD - saves images in the MRC Format compatible with IMOD
- NRRD, Nearly Raw Raster Data - a data format compatible with 3D slicer
- PNG, Portable Network Graphics (*.png) - saves images in the Portable Network Graphics format
- TIF format, LZW compressed, as a multilayered tif-file (3D-Tif option) or as a sequence of tif-files (Sequence of 2D files). Please note! the TIF format uses 32-bit offsets, and that, in practice, limits the maximal size of the TIF-files to 2Gb. Matlab can create TIF files larger than 2Gb but those can't be opened later
- TIF format, non-compressed, see above for details of saving datasets in the TIF format
Make movie
Saves 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
Makes snapshot of the current slice. All objects that are shown in the image view window will be captured. See more here.
Render volume (with Fiji)
Volume rendering of the opened dataset using Fiji 3D image 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:
- Reduce the volume down to, max width pixels - allows to reduce size of the dataset prior the rendering. This reduces memory consumption and improves performance. When this field contains 0 no volume resizing occurs.
- Smoothing 3d kernel, width - smooth the volume with gaussian blur. No smoothing when 0.
- Invert? [0-no, 1-yes] - invert the dataset, required for electron microscopy images.
- Transparency threshold - all pixels with intensities below the provided value will appear transparent. Comma-separated numbers may be used here to provide specific transparency parameters for each color channel. In addition, the transparency threshold can also be tweaked in the Fiji 3D viewer window: 3D Viewer->Edit->Attributes->Adjust threshold.
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, im_browser stores its configuration parameters in a file that is automatically generated after closing of im_browser:
- for Windows - c:\temp\im_browser.mat or when c:\temp is unavailable in the Windows TEMP directory (C:\Users\User-name\AppData\Local\Temp\). The TEMP directory can be found and accessed with Windows->Start button->%TEMP% command.
- for Linux - in a directory where im_browser is installed, or in the local tmp directory (/tmp).
Back to Index --> User Guide --> Menu