Olympus VS120 - Virtual Slide Scanner
All users of this system are required to:
- Receive orientation/training from Jessi or Michael
- Only use their own login accounts (UNC rule)
- Have a complex password and change it every year if
it is >=17 characters (UNC
rules). If <17 characters password must be changed every 90 days.
- Clean up immersion oil off the 60x objective with lens tissue only and
blot gently (never
Kim Wipes on optics)
- Do not reposition or rotate cameras
- Do not change filter or light path controls
- Scan slides with well hardened mounting media
when using curing mounting media
- Blot off excess mounting media. Ensure no
mounting media is above the top of the cover slip.
- Accept that data stored on the system may be summarily deleted after
Information - Fluorescence
The fluorescence light source, the X-Cite
is running off an external power supply. It has been working properly
in this configuration.
- The temporary external power supply on/off switch is the red switch on
the power strip on the bench (Not the usual power switch on the front of the
unit on the top shelf does nothing).
VS120 booking Calendar is
Michael or Jessi for an account)
- When using the 40x objective please ensure that the coverslip thickness
correction collar is correctly set. On the objective the white lines should be lined up for #1.5
coverslips. If you move the correction for your sample please help out other
users by putting white lines back to the aligned position when you are done.
- Lens cleaning: 60x oil objective clean by blotting with lens tissue.
Please do not wipe. For specific cleaning use lens tissue only (never
Kim wipes) and 91% Isopropyl Alcohol or approved coated lens cleaner
(e.g. Sparkle) when necessary. Ask Michael about cleaning details.
- The 2x objective does not image well with CY5 (Who would
- The other scanner: VS200
information and booking
- "Recently" changed:
- Important Information - On May 3, 2020 the system was
restored to its 2018-10-18 state due to a video card failure and C: drive
- Passwords were reverted to what they were in 2018.
Please update your pwd on the system as soon as practical.
- Login accounts created between 2018 and May 3,
2020 were not restored back on the system
- Some scan project profiles may not longer be
- Contact Michael if you would like a pwd reset or
- Old data/profiles/settings on the C: drive may
be recoverable from the corrupted drive. Ask Michael before Nov 2020.
- A 5th fluorescence channel for CY7 has been added to the system.
cubes are for DAPI, FITC, TRITC, CY5 & CY7 like fluorophores.
COVID-19 Mitigation :
- Wash hands before and
after using the system
- Soap and paper towels are provided at the sink in
- ~70% alcohol is for
gently wiping down (NOT spraying) the keyboard,
mouse, joy stick and counter top
- Spray alcohol onto paper towel//kimwipes under bench in
order to prevent droplets floating onto microscope optics
- NEVER spray near or on the microscope
- Please remove your slide trays, boxes, etc.
from the bench area
- Bring your own fresh disposable gloves if you like.
Dispose of them before leaving..
Hygiene tips for microscopes
- 2020-02-13 New network configuration::
- Web browsing and email is now blocked at the VS120
computer. This has been mandated by OIS/ITS since the system runs
- Access to file servers such as
- External web pages (e.g.
and the booking
calendar) are no longer accessible while at the VS120 computer. However
this page microscopy.unc.edu/vs120
is available. Go figure?
- Remote desktop access is still possible to & from the VS120 system.
Contact Michael for details.
X-cite Xylis fluorescence light source was installed on 2018-09-29
- Storage area on the \\minsky.med.unc.edu\vs120 &
\\minsky.med.unc.edu\vs200 server primarily
for the mucus and mouse groups
- Handling Storage
- E: (on slide scanner computer)
- \\ad.unc.edu\med\cf\shared or \\som-fs.med.unc.edu\cf
(AD domain/Onyen required)
- Please don't store image data on the C: drive unless storage is short
on E: or D:
- File server storage is available at:
on how to connect this \\minsky and other file servers
- Please do not store
image data in "desktop", "My Computer", "My Documents", "My Pictures", etc.
The C: drive needs to be kept as free as possible for temporary files
created by the VS120 software. Please use the E: drive or D: drive for
is in 7200s of Marsico Hall
- Known problems:
The field diaphragm needs to be at 75% (Transmitted
light shading correction calibration relies on this setting). It has
been moved to other positions on occasions resulting in faulty scans.
- Neutral Density Filter 6% (ND6) should be in
- The NDF25 (25%) should be out (not enabled)
- LCB (Light Balancing Daylight) should be in (enabled)
- OP is open filter - no effect on light path
The computer may try a network boot which is futile.
- It will either time out and proceed to a C: drive boot
- Or hang forever at the network boot
- If it hangs forever then reboot and press
ESCAPE and choose setup & boot from the 256GByte SSD drive or
contact Michael on how to work on this issue out
- Xylis fluorescence lamp is cutting out -
- Computer is firewall restricted since it runs Windows
- Olympus BX61VS upright microscope stand
- Transmitted light - halogen lamp
- Fluorescence - 5 channel DAPI like, FITC like, Rhodamine like, CY5 & CY7 like
- LED Fluorescence light - X-Cite
- CMOS camera fluorescence - Orca
Flash 4.0 v3 camera C13440-20CU
- Color Camera with Bayer filter for transmitted light imaging
(chromogenic dyes, e.g. H&E)
1 Standard immersion
(carbon) oil (RI=1.51)
For Windows ($free) - OlyVIA 3.2.1
version 2.9 [or OlyVIA 2.9 or later is at
MHmicroscopy domain account is required for access] extract to a temp directory (e.g. use
winzip), run "setup.exe"
and select install English. A good fast viewer, and newer
versions can not
The Olympus ImageJ plugin: Does not support latest VS120 file format (post
April 2016 update of VS120 software)
Full FIJI for processing and quantitation:
- Get FIJI from http://fiji.sc
.vsi with: File --> Import --> Bio-formats - (uncheck all Import
- FIJI - Fiji uses its own local and dedicated Java installation
(and is not such a security risk as the
Windows installed version which hooks into web browsers, etc.
Windows JAVA is not required by FIJI and can be deleted - a good
security practice if it is not needed by other programs).
- Checking the Java version
- You can tell which Java version ImageJ is using by clicking
the ImageJ status bar (below the square tool buttons) and looking for the part that says e.g.
"Java 1.8.0_172 [64-bit]". The relevant number is the one after
"Java 1."—so e.g. "Java 1.8.0_45" or similar indicates Java 8,
while "Java 1.7.0_79" or similar indicates Java 7.
- The current Java version validated for FIJI is 8.0.172
[viz. 1.8.0_172 on double click- yeah
that representation is confusing] as of 2018-10-01
- If Java is older than version 8, then it can be updated
be getting latest full FIJI installation from
http://fiji.sc and reinstalling
- ImageJ component - go to "Help --> Update Imagej ...".
Usually safe to do.
- Other components, e.g. FIJI, JAVA &
Bio-Formats - go to "Help --> Update ..."
- Hit "Manage update sites" button
and check "Java-8" and "Bio-Formats" and leave other
boxes as is
- Hit "Apply Changes" and then hot "Update
jars/ij-1.51s.jar" or similar
- Wait for downloads and restart FIJI
- Note incremental updates to the JAVA engine will be down
loaded and installed. Version updates (e.g. v6. to v8.) usually require
the whole FIJI installation to be reinstalled using the
latest download from http://fiji.sc
- Note the Java update on the Windows task does not
apply to the JAVA installation used by FIJI
- Note: a large number of user images and other user
added directories under the Fiji.app directory can
substantially slow down updating. Move such user
files to another directory.
- FIJI NOTES:
- The current Bio-Formats seems to only open the largest
image in the .VSI file set - Think this has been fixed.
- 64 bit FIJI is usually required to open .VSI files due to
their large size.
- If image is large and computer bogs down, try cropping image
into smaller regions
- In "Edit --> Options --> Memory & Threads..." set "Maximum
memory:" to ~75% of installed physical memory on your
computer, and uncheck "Keep multiple undo buffers"
- Progress bars are minimally present. Many times
nothing seems to be happening when there is processing quietly
occurring. Windows "Task Manager" "Performance" tab will
give an indication of activity and clues as to when to abort and
- Working with these large files can be tedious. An
alterative is exporting images as .TIF files on the VS120
computer. Note .TIF files need to be under ~1GB to be openable in most programs.
With images up to 2 GBytes FIJI/ImageJ may limp along if the
computer has sufficient RAM to hold the uncompressed image. .JPEG2000 is a good alternative
format. Pixel size (e.g. um/pixel) needs to noted before
Managing Memory in Fiji from OME Bioformats group
Using the system:
Network connection to:
Cystic Fibrosis space on School of Medicine server (AD domain - Onyen
account) (e.g. S: shared, H: users, G: groups)
- Like above but with only one drive letter
e.g. Z: which will contain Shared, Groups & Users:
- Disconnect any drive letter connected to
Shared, Users or Groups.
- From "Computer" on
the "Computer" tab hit "Map Network drive"
- Choose a free drive letter
the Folder: box
- Check "Reconnect at sign-on"
- Check "Connect using different
- Hit "Finish"
- Enter "ad\youractualonyen"
and your Onyen password
- Check "Remember my credentials"
- Tips: If you
- Disconnect drive letter
- Log off
- Log in and try again
- Still problems? Try harassing Michael.
\\Minsky file server on the MHmicroscopy domain
(if you do not have an account there ask Michael
to set one up)
- Other servers - please enquire with Michael
Enquiries / Reporting Problems
- Contact Michael or Jessi for assistance