(Updated 2000 Feb 09)
Zeiss Instructions
(Short Form)
For an in-depth explanation for any step, click on the step # to see the corresponding entry in the Long Form of the instructions.
1. Login as user phodis on the O2 (machine name Munich).
2. Switch scanner on (green switch on left side at rear) and wait 2-3 minutes for the lamp to come on and initialization to be completed.
3. Start up the phodis_sc program by clicking Phodis_sc and then selecting the PHODIS SC button on the menu block.
4. Load your negatives emulsion side down.
5. Select Prescan from the Scan menu, and click Start. Adjust the rubber bands to cover the area you want to prescan.Wait until the red BUSY light goes out before proceeding. Click Setup button from the Prescan window if you want to change prescan parameters, such as exposure time, and then press Ok to return to the main prescan menu. Press Start to commence the prescan.
6. From the prescanned display, select the actual area you wish to digitize, and then click Close. The selected area is used for the finer scan.
7. Select Start from the Scan menu, then the corresponding Setup button if you wish to change:
Scan settings
Image settings
8. After checking that the predicted size of the output file and the estimated scan time are reasonable, click Start.
9. Check that the pixel gray level densities are reasonable and that they all fall within the linear region of the digitization by using the Histogram facility. If it is not correct, go back to 7 and reset the exposure time and scan again.
10. To return to PHODIS SC main menu, select Exit from the histogram File menu. Select Prescan from Scan menu to refresh previous prescan, or load new negatives and click Start< /B> on the Scan Prescan window for a new prescan.
11. After all of your scans for the day are complete, exit Phodis SC software.
12. Switch the scanner off to save the lamp.
13. Open a Unix window (winterm) on Munich and type cd demo/img
14. Type ls to get a list of your files
15. Convert your files to mrc format by typing one of the following:
tld2mrc conversion without byte swap, no OD conversion
tld2mrc_bs conversion with byte swap, no OD conversion
tld2mrc_OD conversion without byte swap, with OD conversion
tld2mrc_bsOD conversion with byte swap and OD conversion
(note: you should always convert to OD when you scan EM images. Try using tld2mrc_OD first and see if the converted images can be read wherever they are processed. If not, try tld2mrc_bsOD).
16. Transfer your converted images via ftp to another computer to keep the O2 disk clean.
17. Log out of Munich.
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