Olympus VS120 - Virtual Slide Scanner
- All users of this system are required to:
- Receive an orientation/training
- Only use their own login accounts (UNC rule)
- Have a complex password and change it at least every 90 days (UNC
- Clean up immersion oil off the 60x objective with lens tissue only (never
is in 7200s of Marsico Hall
- VS120 booking Calendar is
Michael or Jesse for and account)
X-cite Xylis fluorescence light source was installed on 2018-09-29
- Lens cleaning: Use lens tissue only (never
Kim wipes) and 91% Isopropyl Alcohol or approved coated lens cleaner
(e.g. Sparkle). Ask Michael about cleaning details
- Known problems:
- 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
- Olympus BX81 stand
- Transmitted light
- Fluorescence - 4 channel DAPI like, FITC like, Rhodamine like, CY5 like
1 Standard immersion
(carbon) oil (RI=1.51)
For Windows ($free) - OlyVIA
version 2.9 [or OlyVIA 2.9 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, but sadly 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 full 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 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 more
- 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. .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:
- Quick startup/shut down
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 Jesse for assistance