Marsico Hall Microscopy Fellowship (MHMF.ORG)

30 Aug 2022 setup   Current setup with robotic slide feeder on the right The VS200 ASW software was upgraded to version 3.4.1 on May 19, 2023 The free viewer for acquired data is OlyVIA (Windows only).  Latest version 5.1 (Windows 11 or 10).  Versions of OlyVIA prior to 3.4.1 will not open data acquired on the VS200 v3.4.1 or later. Obtaining the OlyVIA viewer installation files: On the VS200 slide scanner at  D:\_OlyVIA or similar On the VS120 slide scanner at  E:\_OlyVIA or similar The cf-x.med.unc.edu data transfer computer (152.19.58.44) At D:\_OlyVIA_5.1-31689 Remote desktop Program to  152.19.58.44  and sign on with your Onyen.  e.g.  ad\michael Note that people outside of the MLI/CF Center may need to have their Onyen enabled on this computer.  Ask Michael From the official Evident/Olympus web site (Registration & serial number may be required) DO NOT USE any version of OlyVIA from websites which are not verified Olympus/Evident sites.  E.g. Do not go to "olyvia.software.informer.com", "freedownloadmanager.org", "olympus.informer.com".  These and other sites provide software which contains malware.  Be very careful of where search engine results direct you to.  Notices: The slide scanner system is for use by researchers in the Marsico Lung Institute and their colleagues and collaborators All users are required to receive training or instruction from Michael before using the system Ultimate permission to use the system is at the discretion of the MLI/CF Center Director All users should log in with their own account (local) OlyVIA 4.2.1 free viewer will install on Windows 11! Previous versions of OlyVIA may need to be uninstalled first.  OIS/IT permission may be required. OlyVIA 4.2 is available at the file scanners  or  \\192.168.2.204\vs200 (local account needed for access) File storage reorganization (new 2024 July): Your data files may be deleted from the D: drive of the VS200 computer after 1 month if free storage space is low on D: Questions/Enquiries: Michael VS200 booking Calendar for trained users is here:     VS200 ASW Version 3.4.1 Notes: Load slides into trays with slides pushed to the back and right. Slide label to the back. Load trays into hotel by gently pushing the tray to back and to the left (This is important so that slide presence is reliably detected) Slide and tray selections has changed and is different from the old v3.2 software - see 'Batch Scan' It is OK to store empty trays in the hotel (tall cabinet on the right). When storing trays in the rack under the table please put pink plastic sheet or cardboard between them OlyVIA v3.4.1, the free viewing software, and versions before, does not install on Windows 11.  Get OlyVIA 4.2 to install on Windows 11.

30 Aug 2022 setup   Current setup with robotic slide feeder on the right

VS200 booking Calendar is here:  

Points to note:

• Cleaning off immersion oil:
  • The 60x 1.35NA objective needs to be cleaned if the previous user, or you, used 60x oil objective. 
  • After 60x oil immersion scanning is done the tray will need to be removed (see Exchange Trays) and the oil cleaned off before more scanning can be carried out with other objectives 
  • Objective cleaning mode
• If you encounter problems please note error code, tray number (or serial number), position of where tray was inserted, and "Project" used

• Tray Number	Tray serial number	Height at slide position (um)							z offset (um)	z offset (old)	Status
  		1	2	3	4	5	6	avg
  1	35001739	151	160	157	149	144	144	151	0	0	In service
  2v4	35023858	-14	-6	-10	-6	-1	11	-4	-155		In service
  3	35004731	-81	-69	-57	-35	-15	6	-42	-193	-225	In service
  4	35004733	-52	-65	-64	-51	-32	7	-43	-194	-166	In service
  5	35005150	-64	-51	-36	-1	21	45	-14	-165	-137	In service
  6	35005151	16	22	26	33	47	59	34	-117	-132	In service
  7	35003711	17	34	40	45	48	51	39	-112	-119	In service
  8	35004493	22	26	41	48	51	48	39	-112	-126	In service

• 2025-11-26

• Tray Number	Tray serial number	Height at slide position (um)**							z offset* (um)	z offset (old)	Status
  		1	2	3	4	5	6	avg
  1	35001739	172	156	156	152	169	169	161	0	-1	In service
  2	35001522								-35	20	Recalled
  3	35004731	-55	-46	-29	-6	15	38	-14	-225	-174	In service
  4	35004733	-28	-45	-45	-39	-16	25	-25	-166	-139	In service
  5	35005150	-46	-31	-13	23	46	65	7	-137	-100	In service
  6	35005151	40	41	47	55	69	81	56	-132	-87	In service
  7	35003711	42	58	62	64	68	69	61	-119		In service
  8	35004493	48	54	64	72	74	79	65	-126		In service

• *20x  $1600 calibration slide 2022-12-16
• ** ASW version 3.4.1 2023-05-19 (new tray thickness calibration protocol)

Mapping Drive Letters to servers (connecting to a serer, e.g. \\Minsky or CF-shared or CF-groups):

• See  http://microscopy.unc.edu/shares  on how to connect to e.g.:
  • \\minsky.med.unc.edu\vs200, \\minsky.med.unc.edu\vs120, \\minsky.med.unc.edu\vs320
  • CF-shared, CF-groups,  \\ad.unc.edu\med\cf\shared,  \\ad.unc.edu\med\cf\shared
  • Shared/groups in your department and other file server shared directories

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Important Considerations:

• If you remove a slide tray with any slides with immersion oil present (60x scans) belonging to the previous user or to yourself please:
  • Choose this objective cleaning mode from the home page to bring the 60x to a position where it is easily cleaned. 
  • Blot the 60x objective with lens tissue before starting your scans
  • This will help prevent oil from dripping into the system or onto other slides.
• Hardening mounting media needs to be well cured. No slides with wet media near lenses.  Clean off excess wet mounting by blotting with a tissue or cutting off hardened material with a razor blade.  Slides with mounting media above the level of the cover slip must not be be scanned.  Failure to do this will result in the scanner being unavailable for cleaning and recalibration.
• If the 40x 0.95 NA objective is being used remember to check that the correction collar is set correctly for the coverslip thickness being used.
• Beware: Fluorescent filters without number% (such as DAPI) during Overview or Settings or higher magnification scans will use light intensity of what was last set possible by a previous users.  The light knob will need to be manually turned on during previews.  In contrast filters with a percentage, e.g., DAPI 20%, sets power level to 20% and will turn on lamp automatically. Old DAPI, FITC, TRITC, mCherry, CY5, CY7 are being kept for compatibility (in the future they may be removed). 
• Don't open the left hand door of the system while scanning.  The weight of the open door causes the internal frame to flex.  Flexing will move the image ~5 um and also change the focus - i.e. cause problems.

General Considerations:

• Store scans on the D: drive.  In an emergency data may be stored on E: or C:.  Avoid using the C: drive and desktop.
• Olympus states not to scan directly to mapped network drives.  Scanning to mapped drive letters slows down scanning.  Data corruption is possible when the data stream is disrupted by network traffic jams or transient disconnections.
• Connecting to a server (mapping to a driver letter) e.g. CF Shared, \\minsky.med.unc.edu\vs200, \\minsky.med.unc.edu\vs120, \\minsky.med.unc.edu\vs320
• It is best to scan to D: and copy files later to servers.
• The VS200 software does not work properly when saving to unc network shares of the form  \\minsky.med.unc.edu\VS200  (i.e. network connection without a drive letter)

COVID-19 Mitigations:

• Quick guide & detailed considerations - hygiene tips for microscopes