Olympus Slide Scanner

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This page documents two ways of performing backups and restoring settings for the Olympus Slide Scanners

Restore points contain all the information to get the Olympus Software up and running again in case of problems

Manual backups can be useful in case of other issues, but this was more the 'old' way of doing backups. GLOOR Recommends the first method.

Slide Scanner Manual

Shading correction wizards can be found p85:

Slide Properties File

Working as a Power User

From inside VS-ASW-FL, go to :
Tools → User Rights → Select Active Role → Power User
This requires that you restart VS-ASW FL

Restore Points in Case of Lost Configuration

You can find the restore points in :
\\svfasraw.epfl.ch\PTBIOP-raw\BIOP Backups\Slide Scanners\
Find the slide scanner name you need then go to
***SLIDE SCANNER NAME***\Restore Points

Create a Restore Point

To use them, open the VS-ASW FL software and do the following

1. Acquire → Devices → Create System Restore Point...
2. Select the save location
3. Let the software close and reopen on its own. The file will be created.
4. Move the file to the Restore Points folder in \\svfasraw\PTBIOP-raw\BIOP Backups\Slide Scanners\

Load a Restore Point

To use them, open the VS-ASW FL software and do the following

1. Acquire → Devices → Restore System Restore Point...
2. Select the .srp file and let the software restart
3. Let the software restart

All Slide Scanner Parameters

All the slide scanner settings are located in

C:\ProgramData\Olympus\OSIS\VS-ASW-FL

Manual Backup of all Parameters

1. Make sure you are on a Windows Admin account
2. Make sure the Slide Scanner software is not running
3. Go to C:\ProgramData\Olympus\OSIS\VS-ASW-FL
4. Copy the VS-ASW FL folder into \svfasraw\PTBIOP-raw\BIOP Backups\Slide Scanners\***SLIDE SCANNER NAME***\All Settings

Manually Replace All Parameters

1. Make sure you are on a Windows Admin account
2. Delete the folder C:\ProgramData\Olympus\OSIS\VS-ASW-FL
3. Go to \\svfasraw\PTBIOP-raw\BIOP Backups\Slide Scanners\SLIDE SCANNER NAME\All Settings
4. Copy the latest VS-ASW FL folder back into C:\ProgramData\Olympus\OSIS\

Remote Desktop Connection for Slide Scanner Users

If a user wants to connect to the Slide Scanner Remotely, we need to add him to the authorized users list

Adding a user

1. Go to Windows → System
2. Right Click → Properties
3. Select Advanced System Settings → Remote tab
4. Click → Select Users... → Add...
5. Enter the username and click Check Names
6. Press OK

User profiles that cause Olympus Software to crash

It has happened with users who were Masters students and became affiliated as PhDs that their Active Directory Identities and settings were not properly changed, namely the folder where their personal data is stored at EPFL.
If when you go manage the user profiles in Windows
Control Panel → System and Security → System → Advanced System Settings → User Profiles → Settings and you see that the user in question has a roaming profile, then contact the IT department to check why that is.

Students have roaming profiles, not PhDs.

Fixing it

When a student changes affiliation, it can happen that there are leftovers of this roaming profile.

1. Login as as administrator
2. Delete the user profile
3. Have the IT fix the user entry
4. Let him log in again. He should have a 'local' profile then.

A less violent approach

A protocol given to José by Gloor suggest the following

1. Close the Software
2. Go to C:\Users\**UERNAME**\App data\local\Olympus\OSIS\
3. Rename VS-ASW FL to something else, like VS-ASW FL_Old
4. Restart the software. The folder will be recreated automatically with the settings from C:\ProgramData\Olympus\OSIS\VS-ASW-FL

Defining the folder where overviews are stored

Some users have noticed that Slide Scanners are crashing during overview acquisitions because it takes a huge amount of data in the app data folder on C.
It is possible to change the default storage location for these overviews by following the instructions here :

https://docs.google.com/presentation/d/1qZtQCQMq3iyPJjH3xfSj80Nq4rhx1Deb4Bb5vhSZd94

Automatic deletion of overviews upon user Log Off

A windows bash script is present on both slide scanner in order to automatically delete the overviews stored on the C Drive. A copy of these script can be found here (and bat files are in the root folder):

https://docs.google.com/document/d/1rzrZD-CMExV3FmqoQ4kAfCe_agTQKTXy1obGBjqAPrM/edit

You can activate or deactivate this scripts by following the instructions here (https://www.nextofwindows.com/how-to-run-a-script-or-command-at-logoff-in-windows-7-8)

Fixing shifts between BrightField Overview and precise acquisition

If the xy shift between different objective magnifications (2x, 4x, 10x, 20x, 40x) is not properly calibrated, there will be a systematic shift observed between the overview of the slide and the precisely acquired camera. Focus points can thus also be set at wrong locations (i.e., where is no feature present to make the focus).

In order to solve, this, one needs to re-calibrate the XY Objective Shift(s) of the slide scanner.

Here's the step by step procedure to perform this calibration:

• using manual loading, put a slide with a strongly contrasted sample for BrightField imaging - sufficiently large (about 1cm wide). A full FOV of the 2x objective needs to be covered
• Select the BrightField (BF) illumination mode on the top right part of the software. You can then click Live to focus the sample and check that, at the magnification of 40x, some structures will be present.

• Click on the top menu Acquire → Calibrations...

• Choose the camera to align. For the shift between overview in BF and the color camera, it will be VC50 → XY Objective Shift / Parfocality
• Click Calibrate...
• Check All objectives, uncheck Calibrate Z parfocality (it is expected that the parfocality is correct), but keep Calibrate XY objective centering checked.

• and click Next

The sequence of acquisition for each magnification starts. Normally, of the sample is contrasted enough, you'll be able to just click next for each magnification, leading to a sequence of image looking like the one below:

• At the end of the wizard, you have the new applied corrections shifts, that you decide to keep or discard:

If the camera is not recognized

This happens sometimes after a windows update. The camera driver is overriden by a microsoft one.

You can use the utility from Leica to restore the proper camera driver.

In the end, the device manager should look like this: