SOP of Slide Scanning

Table of Contents

1. Purpose

2. Safety Requirements

3. Associated Documents

4. Notes

5. Equipment

6. Supplies

7. Procedures

1.Purpose


1.1 : An automatic digitalization of histological sections will be provided. Sections obtained from biological specimens and samples of human or animal bodies on standardized slides can be shown by either transmitted light mode or reflected light
fluorescence mode.

2. Safety Requirements


2.1 : General laboratory procedures should be followed, which include: no eating, no chewing gum, no drinking, and no applying of cosmetics in the work area. Laboratory coats and gloves must be worn at all times in the work area, unless the protocol specifically describes the appropriate attire for the procedure.

3. Associated Documents


3.1 : Appendix :MIRAX VIEWER Operating Manual
                       MIRAX VIEWER Software
After download MIRAX Viewer software, run MIRAX Viewer (do not choose Setup, Setup is used to repair/delete program)
During installation, there is a choosing window:
Choose “Install MIRAX Viewer as a free viewer with limited functions”,
Then keep choosing “next” to complete installation.

4. Notes


4.1 : The standardized slide should be 75.0 to 76.2 mm in length, 25.0 to 26.0 mm in width and 0.95 to 1.05 mm in thickness.
4.2 : The coverslip, max. 50 mm in length, max. 24 mm (recommended 22 mm) in width and 0.13 to 0.19 mm in thickness.
4.3 : Three standard fluorescence filter cubes are offered. The wavelengths of excitation and emission filters are listed as following:
(i) Filter set 1: Ex. 350/50 and Em. 460/50 which is suitable for the observation of DAPI, Hoechst and etc.
(ii) Filter set 2: Ex. 470/40 and Em. 525/50 which is suitable for the observation of GFP, FITC and etc.
(iii) Filter set 3: Ex. 545/30 and Em.620/60 which is suitable for the observation of Cy3, Rhodamine and etc.
4.4 : If the fluorescence specimen needs to be scanned, some precautions should be noticed:
(i) The anti-fading reagent should be added to mounting reagent.
(ii) Do not use neither nail polish to seal the slide corner nor contain glycerol only mounting reagent.
(iii) Please use the mounting reagents that harden as they dry.
(iv) Counter stain should be done.

5. Equipment


5.1 : MIRAX SCAN, ZEISS
5.2 : Digital Camera, Marlin
5.3 : HXP 120 Compact Light Source, LEj
5.4 : PC, Fujisu Siemens Celsius R650
5.5 : Monitor, Dell
5.6 : Metal Magazine, Zeiss

6. Supplies


6.1 : Histological sections
6.2 : Wiper
6.3 : 70% alcohol
6.4 : DVD

7. Procedures

The Mirax Scan is able to work in automatic and manual modes for both brightfield and fluorescence application. Choose the scanning mode needed and follow the appropriate procedures.

7.1 : Turn on the power of MIRAX SCAN, PC and monitor.
7.2 : Double click the MIRAX software icon on the desktop or click on Start →Programs →Carl Zeiss →Mirax Scan alternatively to initialize motors, the preview camera and the scan camera.
7.3 : Choose the scan applications which is either Brightfield or Fluorescence on the selection window.
7.3.1 : Select either Automatic and Manual for both of brightfield and fluorescence options.
7.3.2 : Automatic mode should be used when section slides are large in number.
7.3.3 : (i) Manual mode is used only when individual slide need to be digitized.
          (ii) Special stain or parameter need to be determined.
7.4 : Insert the slides into the magazine and fill some empty slides on the other side of the magazine. This is to prevent the magazine from topple over.
7.4.1 : Transport the filled magazine without its cover on it into Mirax Scan.
7.5 : For Brightfield and Fluorescence manual :
Insert magazine and select Routine work
7.5.1 : Select the slide position to digitize the slides.
7.5.2 : Preview the slides.
7.5.3 : Adjust the thresholding and other settings if necessary. Choose scan filter for fluorescence manual scanning.
7.5.4 : Enter the slide name.
7.5.5 : Save scan profile.
7.5.6 : Select Start scan.
7.5.7 : Select output slides and remove magazine.
7.6 : For Brightfield and Fluorescence automatic:
Insert magazine with slides and there is a pre-typed profile available. For Fluorescence, turn on HXP 120 Compact Light Source.
7.6.1 : Select Barcode
7.6.2 : (i)Enable Read barcode if no name is defined on the list
          (ii)Enable Generate name if no name was defined
          (iii)Enter designations into table
7.6.3 : (i) Select profile under Apply one profile to all slides if there is a profile used
          (ii)An individual profile can be used for each slide in the second column.
7.6.4 : Select First and Last slide that need to be digitized.
7.6.5 : Change scanned slide to different folder under Scan option if necessary.
7.6.6 : Select Start scan.
7.6.7 : Select output slides and remove magazine.
7.7 : Terminate all the program.
7.8 : Close Mirax software.
7.9 :Turn off the power of Mirax Scan, PC, monitor and light source.