Microscopes

The Laboratory offers imaging services on two laser scanning fluorescent microscopes, a Bio-Rad Radiance 2100 MP Rainbow confocal/multiphoton microscope and a Bio-Rad MRC-1024 confocal microscope. Click on the equipment pictures for a detailed description of each system.

Radiance 2100 MP Rainbow
Confocal/Multiphoton System
Room 52 MSC
MRC-1024
Confocal System
Room 52 MSC


File Transfer

Files from the Bio-Rad 1024 are easily transferred using the Laboratory's FTP site. (Images from the Bio-Rad Radiance must be copied to a portable USB drive/memory stick or burned to CD.) Files first must be uploaded to the site from the microscope computer, and then can be downloaded to any desired computer.


To download using Windows:

1. Open Windows Explorer (not Internet Explorer).
2. In the address bar, enter: ftp://keck.bioimaging.wisc.edu/
3. Enter the username and password provided by Keck staff.
4. The contents of the FTP site should appear. Simply find the folder into which the files were uploaded and copy them ("drag-and-drop") to the desired folder on your computer.


To download using Mac OS:

1. Download and install the FTP program FileZilla.
2. Run the program and use the following settings:

Host: www.keck.bioimaging.wisc.edu
Username: (provided by Keck staff)
Password: (provided by Keck staff)
Port: (leave blank)

3. The right side of the interface is the FTP site ("Remote site") and the left side is the computer currently being used ("Local site"). The upper side-by-side boxes show the directory tree, and the lower side-by-side boxes show the contents of the current folder. Simply locate the files previously uploaded to the FTP site on the right side and then drag-and-drop them to the desired folder on the left side.


Working with .ND2 Files (Nikon A1)

The .nd2 file format is Nikon's proprietary format for image data. Each file contains either a single (multi-channel) image or a series of images (from a spectral, time, and/or z-series). Also contained are the metadata associated with an image or image series, such as the microscope settings used.
  • NIS-Elements Viewer (Version 3.2 for Windows | Version 4.11 for Mac OS X)
    The Viewer is the best program to view your files and associated metadata. You can also export images as TIFs for use elsewhere.

  • ImageJ (Fiji Bundle with Bio-Formats Plugin)
    ImageJ has numerous functions for data display, analysis, and export. However, to open .nd2 files properly, the very newest version of the Bio-Formats plugin ("loci_tools.jar" file) must be downloaded and saved to the Fiji "plugins" folder.