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How to use the Zeiss Scanner

To start

Switch on scanner – switch is on the left towards the back. When the LED display says 'self test OK' and the red 'busy' light is out the scanner is ready to use. Wearing cotton gloves for cleanliness, open the scanner hood and lift the top glass plate. (Be careful not to let it fall from its fixing and crash onto the bottom plate). Place the film(s) on the bottom plate with the emulsion side facing DOWN. 6 negatives can be fitted on the glass plates. Close the glass lid and scanner hood. Switch on the PC if not already on To start the scanning software start Photoscan TD (Start, Programs, PhotoscanTD, Photoscan TD or icon on desktop). There are icons on the tool bar for many of the following operations. These instructions refer to the menu. Do …


New Scan



Scan Properties

There are three pages to set up: Scan setup , Film output and Camera Setup.

  1. Scan setup read in def_setup_par as a template. Then rename it for your own use. Gray-scale – go to advanced: Best to use the green band for grayscale. Set resolution such that the desired area of the micrograph can be identified (224um to view a large area, 56 um to see a micrograph in more detail). Once the desired area has been found use 7um for a full scan.
    • Tile size: 256
    • Format: Tif uncompressed
    • Overview: use full set
    Image file: give it a name E:/scans/yourname.tif (or use scratch disk Z:/ - see File storage and backing up section for instructions). Save the parameter file for future use.
  2. Film Output Select transmissivity name the file – same name as for scan setup can be used scan gamma correction – make sure NOT highlighted
    • Film polarity negative
    • Output polarity positive
    Save the file
  3. Camera setup Select either Right-reading film.par or Wrong-reading film.par. (has the effect of flipping the film i.e. will reverse the hand.)

The following instructions apply if you want to scan several films and you don’t want to prescan each time. To prescan the film:

  • Scan Properties
  • Read in parameter files appropriate for your films
  • Set resolution on scan setup to 224 um and give your prescan IMAGE a filename.
  • Use the yellow 'rubber bands' to select a large area over the glass plates which will include all the micrographs you have placed there.
  • Do… Scan Scan to disk Or… click on the blue 'scan to disk' button on the tool bar.
  • Wait for it to finish scanning (red 'busy' light goes out on scanner) If the micrographs are visible, fine. If not, you need to adjust the histogram which appears as a new page. There are 4 ways of adjusting the histogram:
    1. fit
    2. 1%
    3. Manual – click mouse on histogram, drag and release
    4. go into Film Output and type in transmisivity values e.g.  Neil's CM200 images required 0.0178- 0.085 film transmisivity values reset gets back the original histogram. Apply sets the values for the next scan.
    If you cannot see the area you want properly, try a second prescan at 56um.

For the full, final scan:

  • Now select the first micrograph on the prescanned image.
  • Do ... View Fit image Click on the image ... To get it all in the window.
  • Then ... View Define scan area Click and hold the button down on the first micrograph to get the first corner. Then drag and release to get a rectangle. Even though the rectangle vanishes when you release the mouse button the area is still selected. It shows up in yellow on the scan setup page. Go to Scan set up and change the filename but don’t save it this time. Change the resolution to 7 um and the IMAGE filename to what you want to call the image. DO NOT save the parameter file this time. The filename can be left blank. Click on ‘Scan to disk’ again. It will ask if you want to save your prescanned image. Say yes! A 7um micrograph took around 8 mins
  • When the image is scanned check that histogram is satisfactory, reset if necessary, and rescan if not OK.
  • At this stage the image is NOT SAVED! To save the image you have to close the image window and wait for it to ask you if you want to keep the image and say yes!

Now to scan the next micrograph do...

  • File
  • Open Raster
  • Browse to find your prescanned image
  • Select another region, if necessary prescanning at 56 um.
  • Go to scan properties and change the image filename and check the parameters e.g. resolution = 7um. Check all the other parameter files.
  • Click on 'scan to disk'
  • When this image is scanned... Close the window and save the new file Go back to ... File Open Raster get the prescanned images back and select and scan once more.

To switch off

The policy is to leave the scanner on during the day but switch if off at night. Leave the computer on. You dont need to switch off the computer to switch the scanner on again.

File storage and backing up

Scanner scratch disk

The scanner scratch disk can be seen from the unix system or from Windows NT (see below). The disk will be automatically purged each night to keep it below 75% full. This will leave about 9Gb of disk space free each morning, which is about as much as you can scan in a day on the zeiss scanner. This of course means that your files are NOT SAFE on this disk, and can be deleted without warning by the system software, and back-ups WILL NOT BE MADE OF THIS DISK! It would be best if you deleted your files from the disk ASAP so that it does not become necessary to rely on the purger.

1) Accessing the scratch disk from Windows NT

Open a command prompt window (from the programs menu) and type (exactly)...

net use Z: \\kea\scanner

then enter your unix password. This will mount the new disk on NT as drive Z:. You can then use this disk just like any other, even scanning files straight to it. This should be quicker and simpler than FTP. Also, NT should remember this connection and remake it when you next log into any NT machine, so we effectively now have a group I: drive which you can see from your own computers too. In fact, you can use the above command from your own PC and start using the disk now. If you're only doing a couple of scans, there's a CD-writer on the scanner's PC, so you can still back up to CD.

2) Accessing the scratch disk from unix

This drive can be found at:


The disk is mounted on kea, so use kea to convert tif files to mrc (using /s/spider/tiff2mrc/tiff2mrc.exe).

Backing Up

Use the dds-3 DAT drive (with a dds-3 tape!) on longa to backup your scans onto tape. The tapes hold 12Gb uncompressed. MRC format files compress by about 15% only, so that might go up to about 14Gb. Delete your scans from hs43.

Converting Files

To convert the tif format files to MRC use tiff2mrc.exe in /s/spider/tiff2mrc/. If you wish to convert a series of files you can use the script... tiff2mrc_series_ap which, as long as you put your scans in a sensible image series e.g.… name0001.tif--- to name9999.tif..(any number of digits is possible), then the whole series can be converted to mrc in one go.



Use optical cleaner to clean plates, especially the bottom ‘image carrier’ plate, every 2-3 days or if it needs it. Best not to use sprays to blow off dust as can leave drops  of liquid. Need to clean the normalisation patch once a week (Corinne, Neil, Uli and Dan know where this is): To get at the patch switch the scanner on and wait for ‘searching for ref’. After 2 secs open the lid. The scanner arm will have moved off the patch and you can get at it. Blow dust off with a rubber ‘puffer’, rather than spray, and wipe the surface with a q-tip wetted with water or optical cleaner. Then dry the surface. Then put hood down. It will say ‘self test/normalisation failed’ Just reset it to carry on.

Defragmentation program

‘Defrag’ should be run once a week to free up disk space. Need to choose a drive first and then run.

Changing the bulb.

Switch the scanner off Use the alan key in the tool kit to undo the lamp housing. Let the lamp cool a bit. Pull clip off the back of the lamp (looks like two pieces but is only one) Wearing cotton gloves so you don’t get fingerprints on the bulb, ease lamp out. Click new lamp into place. Slide the lamp housing back in.

Further Information

The Hyperterminal program tells you what is going on in more detail. You can look at it while the scanner is switching on etc and if there are any problems. If there is a problem cut and paste the readout and save it. Signs of health: While normalising ‘FF values’ should be 0 for blue, green and red. Min and Max should not differ by more than 80. Also for ‘No. of O-values’ blue, green and red no zero values. Max value should never exceed 15. Difference between min and max should also not exceed 15. There is no need to normalise the scanner manually. It has been set to renormalise every 45 minutes (without interrupting a scan). Lamp integration time should be between 1.5 and 2.5 ms. If longer lamp needs replacing. If you have a problem check: Control Panel, SCSI adapter icon, Devices, should see Carl Zeiss Scanner. 75-85°F is preferred temp It is possible to convert the output file to a raw image. Start, Program, Image Station, Raster Utilities, Raw File Converter. Use ’add’ to select a file. If you want to delete a parameter file… you need to delete scan setup file before deleting film output file or it gets confused.