Using the PDS 1010GM Microdensitometer

Download MSWord file with these instructions: PDS-1010GM-Usage.doc

Contents

To start

• Put on gloves
• Sweep glass with anti-static brush
  • do not use canned air on glass
• Clean film with quick burst of canned air
• Place film on glass emulsion side up
• Plug in vacuum pump for film holder
  • pump located on other side of the wall but plug comes through the wall

PDS Alignment

• Select "7" on inner filter wheel (protects PMT)
• Turn on Power, Lamp, PMT and allow to warm up
• Select upper and lower apertures and lenses depending on required pixel size
  • i.e. For 13 um scan:
    • Use "B" aperture" and "2" lens both above and below the film
  • For 6.5 um scan
    • Use "B" aperture and "4" lens above and below the film
• Move to clear area on film
• Focus lower lens until see sharp edges of lower aperture on screen
• Remove aperture with lower left dial
• Focus upper lens until film grain is sharp (not lamp fiber optics!)
• Replace aperture
• Center upper lens roughly on main screen- with 4 set screws
• Check center with monocular (upper aperture should be inside lower aperture)
• Set gain:
  • Select "C" on filter wheels (both)
  • Toggle to TRANS, CALIB to 1
  • adjust PMT voltage -> 1.00
• Toggle to DENS, CALIB to N
  • adjust LOG -> 0.06
• Leave in DENS - N mode
• Select "7" on inner filter wheel for safety - especially with small apertures
• Move to center of desired scan
• Reset X-Y positions with red push buttons
• Remove aperture with lower dial
• Check lens focus on film grain using monocular eyepiece
• Replace aperture
• Select "C" on filter wheel
• Push SELECT -> AUTO

Computer Controls

• Put computer in MSDOS mode
  • Either choose MSDOS mode upon startup
  • Or choose "Shutdown" and specify "Start in MSDOS mode"
• Start SCANS-A-LOT control program
  • cd c:\pds
  • scans
• look over configuration, press ENTER
• Enter "ED" to edit scan
• "2" to change name of file
• "3" to change scan parameters and speed
• "ctrl + Z" to go back to edit menu
• "0" to exit out of edit menu
• "h" to display Scans-A-Lot prompts
• "CS" to begin scan
• "Q" to exit to windows

Finish scan

• Turn off PMT, Lamp, Power and recover PDS when finished

Transfer files to dl380

• start Windows
  • type "win" at MSDOS command prompt
• click winscp361.exe
• Copy files from c:\pds on PDS computer to dl380 /home/your file folder
  • Via drag and drop
• Delete files from PDS computer after confirmed transfer

Visit Cryo EM Web site at http://www.nysbc.org/facilities/CEM

-- DavidStokes - 18 Mar 2005

Download MSWord file with these instructions: PDS-1010GM-Usage.doc

Contents

To start

• Put on gloves
• Sweep glass with anti-static brush
  • do not use canned air on glass
• Clean film with quick burst of canned air
• Place film on glass emulsion side up
• Plug in vacuum pump for film holder
  • pump located on other side of the wall but plug comes through the wall

PDS Alignment

• Select "7" on inner filter wheel (protects PMT)
• Turn on Power, Lamp, PMT and allow to warm up
• Select upper and lower apertures and lenses depending on required pixel size
  • i.e. For 13 um scan:
    • Use "B" aperture" and "2" lens both above and below the film
  • For 6.5 um scan
    • Use "B" aperture and "4" lens above and below the film
• Move to clear area on film
• Focus lower lens until see sharp edges of lower aperture on screen
• Remove aperture with lower left dial
• Focus upper lens until film grain is sharp (not lamp fiber optics!)
• Replace aperture
• Center upper lens roughly on main screen- with 4 set screws
• Check center with monocular (upper aperture should be inside lower aperture)
• Set gain:
  • Select "C" on filter wheels (both)
  • Toggle to TRANS, CALIB to 1
  • adjust PMT voltage -> 1.00
• Toggle to DENS, CALIB to N
  • adjust LOG -> 0.06
• Leave in DENS - N mode
• Select "7" on inner filter wheel for safety - especially with small apertures
• Move to center of desired scan
• Reset X-Y positions with red push buttons
• Remove aperture with lower dial
• Check lens focus on film grain using monocular eyepiece
• Replace aperture
• Select "C" on filter wheel
• Push SELECT -> AUTO

Computer Controls

• Put computer in MSDOS mode
  • Either choose MSDOS mode upon startup
  • Or choose "Shutdown" and specify "Start in MSDOS mode"
• Start SCANS-A-LOT control program
  • cd c:\pds
  • scans
• look over configuration, press ENTER
• Enter "ED" to edit scan
• "2" to change name of file
• "3" to change scan parameters and speed
• "ctrl + Z" to go back to edit menu
• "0" to exit out of edit menu
• "h" to display Scans-A-Lot prompts
• "CS" to begin scan
• "Q" to exit to windows

Finish scan

• Turn off PMT, Lamp, Power and recover PDS when finished

Transfer files to dl380

• start Windows
  • type "win" at MSDOS command prompt
• click winscp361.exe
• Copy files from c:\pds on PDS computer to dl380 /home/your file folder
  • Via drag and drop
• Delete files from PDS computer after confirmed transfer

Visit Cryo EM Web site at http://www.nysbc.org/facilities/CEM

-- DavidStokes - 18 Mar 2005

Download MSWord file with these instructions: PDS-1010GM-Usage.doc

Contents

To start

• Put on gloves
• Sweep glass with anti-static brush
  • do not use canned air on glass
• Clean film with quick burst of canned air
• Place film on glass emulsion side up
• Plug in vacuum pump for film holder
  • pump located on other side of the wall but plug comes through the wall

PDS Alignment

• Select "7" on inner filter wheel (protects PMT)
• Turn on Power, Lamp, PMT and allow to warm up
• Select upper and lower apertures and lenses depending on required pixel size
  • i.e. For 13 um scan:
    • Use "B" aperture" and "2" lens both above and below the film
  • For 6.5 um scan
    • Use "B" aperture and "4" lens above and below the film
• Move to clear area on film
• Focus lower lens until see sharp edges of lower aperture on screen
• Remove aperture with lower left dial
• Focus upper lens until film grain is sharp (not lamp fiber optics!)
• Replace aperture
• Center upper lens roughly on main screen- with 4 set screws
• Check center with monocular (upper aperture should be inside lower aperture)
• Set gain:
  • Select "C" on filter wheels (both)
  • Toggle to TRANS, CALIB to 1
  • adjust PMT voltage -> 1.00
• Toggle to DENS, CALIB to N
  • adjust LOG -> 0.06
• Leave in DENS - N mode
• Select "7" on inner filter wheel for safety - especially with small apertures
• Move to center of desired scan
• Reset X-Y positions with red push buttons
• Remove aperture with lower dial
• Check lens focus on film grain using monocular eyepiece
• Replace aperture
• Select "C" on filter wheel
• Push SELECT -> AUTO

Computer Controls

• Put computer in MSDOS mode
  • Either choose MSDOS mode upon startup
  • Or choose "Shutdown" and specify "Start in MSDOS mode"
• Start SCANS-A-LOT control program
  • cd c:\pds
  • scans
• look over configuration, press ENTER
• Enter "ED" to edit scan
• "2" to change name of file
• "3" to change scan parameters and speed
• "ctrl + Z" to go back to edit menu
• "0" to exit out of edit menu
• "h" to display Scans-A-Lot prompts
• "CS" to begin scan
• "Q" to exit to windows

Finish scan

• Turn off PMT, Lamp, Power and recover PDS when finished

Transfer files to dl380

• start Windows
  • type "win" at MSDOS command prompt
• click winscp361.exe
• Copy files from c:\pds on PDS computer to dl380 /home/your file folder
  • Via drag and drop
• Delete files from PDS computer after confirmed transfer

Visit Cryo EM Web site at http://www.nysbc.org/facilities/CEM

-- DavidStokes - 18 Mar 2005