(Updated 1999 Nov 03)
Zeiss Scanner
Instructions for use
Some general rules:
always log in to the SGI O2 first and then switch scanner on
never open the scanner lid when the red busy light is on
never click Break on any window or bad things may happen (to you)
clean the glass surfaces with lint free cloth and the Windex provided:
inside surfaces of glass and top surface of top glass only -- if the outer surface of the bottom glass plate needs cleaning let Linda or Niko know and they will help you
additional maintenance will be done by Linda Melanson or Niko Grigorieff
1. Log in 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. Do this before starting the phodis_sc program. When the machine is ready the red busy light will go out, and Self test OK should appear on the SCANNER LCD. (Note: Never open the scanner hood when the LCD says BUSY.)
3. Start up the phodis_sc program by clicking Phodis and then selecting the PHODIS SC button on the menu block. This action connects the Compaq and SGI computers, and the LCD readout on the scanner will now indicate that they are connected. (You can also run the program by typing psc in a UNIX window.) Once you are in the Phodis menu it means that both the Compaq and SGI computers are connected.
4. Open the scanner lid. Clean the glass plates with Windex and a lint free cloth. Carefully remove dust from your pictures and put all the negatives you want to scan between the glass plates with the emulsion side down. (For SO163 film the emulsion is facing you when the film notch is upper right.) You can load six 3.25 x 4 inch negatives at one time but be sure to leave some space (about 1 inch) from the perimeter of the glass plate. Once negatives are loaded, carefully lower the glass plate FIRST and THEN close the scanner lid. Do not re-open until the negatives are to be removed.
Normalization of the CCD is to adjust the gain of each pixel is automatically done when the scanner is switched on. To normalize again, (only necessary 2 - 3 hours after scanner start-up) choose CCD normalization from the Scan menu or Scan Device (under Tools) menu.
5. Select Prescan from the Scan menu. Adjust the rubber bands to cover the area you want to prescan, and click Start. This carries out a rapid, very coarse scan of the entire area using 224 um pixels, and leaves a picture of your negative(s) on the screen. Wait until the red BUSY light goes out before proceeding. Click Setup button from the Prescan window. This opens the Setup Scan window where you can change parameters for the prescan, such as exposure time (longer exposure times correspond to brighter images; shorter times correspond to darker images). To change exposure time, activate the Exposure time field (only pink fields are active) by clicking with the left mouse button and typing the desired exposure time. Be sure to press carriage return so that the changed values are accepted. Press Ok to return to the main Prescan window.
Hint: Rather than playing with the exposure time for the prescan, one can choose the Scan option for LUT (lookup table) from the setup menu rather than the default 1:1 mode. This allows through a rather wide dynamic range. Make sure the fine scans are done in 1:1 mode though; we don't know exactly what Scan mode is doing.
6. From the prescanned display, select the actual area you wish to digitize with the rubber bands, and then click Close (not Start -- that'll restart the prescan). 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:
Under Scan settings
Resolution -- use 7 um. The scanner does weird things at coarser rasters.
Scan area -- for example, the scanned area will be 6000 x 6000 pixels if an area of 42 x 42 mm using 7 um pixels is selected.
Exposure time -- This updates the exposure time. Remember, if you don't press carriage return, the value will be reset to whatever value was set in the prescan setup window (see step 5 above).
Lookup table (LUT) should be in the 1:1 option (this is the default)
Under Image settings
Filename -- i.e. PHO_IMG/filename.tld
Description
Choose tld for the Storage format
Select Display image after scan.
8. After checking that the predicted size of the output file and the estimated scan time are reasonable, click Start. A time bar will show time passing but wait until the red BUSY light on the scanner goes out before proceeding.
9. If display after scan has been selected, the image will appear on the screen when the scan has completed. If you move the cursor onto the image, a red box will appear. Clicking the right mouse button will open a menu, with which you can zoom, go to a 1:1 display, go back to the original image size, or exit which sends you back to the PHODIS_SC menu.
Go to the Image View window and select Histogram from the Config pulldown menu. Check that the pixel grey level densities are reasonable and that they all fall within the linear (i.e., middle) region of the dynamic range by looking at the histogram. If the histogram bell curve is somewhere in the middle, proceed to step 10. If not, repeat step 7 above.
10. To return to PHODIS SC main menu, select Exit from the histogram File menu. Select Prescan from the Scan menu to refresh previous prescan, or load new negatives and click Start on the Scan Prescan window for a new prescan.
11. After all of your scans for the day are complete, select Exit from the File pulldown menu of the PHODIS SC window to exit from Phodis SC software. The Exit Program window will say, "Actual parameters changed! Save now?" Select "No." (Selecting "Yes" will give a permission-denied type of error.)
12. Switch the scanner off to save the lamp. (Lamp lifetime is about 200 hours.)
13. Open a winterm Unix window on Munich and type cd demo/img (a Unix window can be opened by selecting Open Unix Shell under Desktop in the Toolchest menu)
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. The byte swap option may have to be used if the converted images are processed on a computer which is not an SGI. 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. For example:
Munich % ftp shiva
name:(shiva:phodis): your_user_name
password: your_password
ftp> binary
200 type set to I (I = image as opposed to ascii format)
ftp> cd your_directory
ftp> put filename (to move one file)
(or ftp> mput file* (to move multiple files))
ftp> bye
17. Log out of Munich. Select Log Out from the Desktop pulldown menu form the main desktop window, or hold down the right mouse button and select Log Out.
Other useful phodis_sc tips:
Initialise in the Tools/Scan device menu does a full scanner reset
Reset does a more limited reset keeping some tables CCD-normalise carries out a dark current + gain calibration of the 5632 pixels of the CCD. Will be done automatically, but the more anal can do it whenever the urge comes.
Other relevant UNIX commands:
scaiterm opens a new window with a SCAI icon and gives the command line "cu -l ttyd2" which starts up a procedure which monitors the traffic between the Compaq and the O2 passing through the serial port. This can give some interesting diagnostics.
od -F ((Calib.dat ) binary octal dumps of the positional calibration - CALIB.DAT ) may be needed later. calibration.dat (ascii version)
scmb_test direct (non GUI) communication with PC. For example allows up and downloading of calibration data CALIB_U and CALIB_D. Dangerous to use.
ipcs interprocess communication status - flags queues, shared memory and semaphores etc. There should be none left after quitting the phodis_sc program.
swap -s examine available swap space. With no program running, there should be 10-13 Mbytes used out of 200 Mbytes available.
shmkill shared memory kill, can get rid of left over bits of unused memory in case of some kinds of crashes.
tld.h and tif.h in area /disk2/PHODIS/pho_lib are include files which may help to understand the tld and tif file formats as they are used by phodis_sc.
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