Microscope Introduction
The Epifluorescence microscope in the microbiology laboratory aboard the JOIDES Resolution consists of a Zeiss Axio Imager 2 microscope with transmitted and reflected capabilities as well as a CoolLED pE-100 single wavelength illumination systems for screening fluorescence. The microscope is furthermore outfitted with a Zeiss 506 cam for imaging and the ZEN lite software.
Cool lights usage
First, switch on the microscope lights and select RL/3200 K:
LEDs are switched on and off by pressing the ‘on/off’ button. At start-up the Light Source will revert to the same settings that were set when it was last powered down. New Light Sources are supplied with the settings as shown.
Adjust the intensity of the Light Source by pressing the up and down intensity buttons. This is displayed in 1% steps between 20% and 100%. Between 0% and 20% this figure is displayed in 0.2% intensity steps.
Camera/Imaging
The microscope has a Zeiss 506 color camera attached and has Zen lite software installed. the sensitivity of the camera is based on a 6 megapixel CCD sensor and has a resolution of 2752 horizontal pixels × 2208 vertical pixels.
(Graph source: zeiss.com)
Zen blue (image acquisition software)
1) Find either the desktop or toolbar Zen button after the camera is plugged in and click it to open.
2) This is the user interface:
1 - Left Tool Area: With the tabs you can access all the main tools for microscope control (Locate Tab), acquisition (Acquisition Tab), image processing (Processing Tab), image analysis (Analysis Tab), and applications (Applications Tab).
2 - Center Screen Area: This area is used to display your images with several image views available.
3 - Right Tool Area: Here you find the Images and Documents Tool, the Objective Selection and the Stage and Focus controls.
3) On the left side in the tool area, the Set exposure/Live/Continuous and Snap will become active a few seconds after opening the software. Click Live, be sure to set the microscope light path to the camera (see picture). A live image will be displayed in the center area of Zen blue.
4) In the Left Tool area the user can set all microscope components to the correct settings in order for the metadata to be saved once ready for image acquisition.
5) In the same tool area to the left, the camera settings can be adjusted (exposure time etc.).
6) When ready, click Snap. The software will take a picture and display it as .czi file in the central screen area.
7) In the Processing tool, pick the Method Image Export and select JPEG filetype, Export to C:\data\in and Generate xml file, then click Apply. When the user closes the program, it will ask if the original .czi file should be saved as well - please confirm and save in the same folder.
8) IODP is developing an uploader tool for these images. Until then, save the images on Uservol/Microbiology/Microscope_images.