olympus vs110-s5 slide scanner – standard operating procedure · olympus vs110-s5 slide scanner...

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Olympus VS110-S5 Slide Scanner – Standard Operating Procedure

STARTUP SEQUENCE

1. X‐Cite lamp (for fluorescence, 10 min warmup)

2. IX2‐FCB (Filter wheels for fluorescence)

3. Controller (BX‐UCB large white box)

4. Computer

5. Login: UserVS110 account (no password)

6. Double click VS‐ASW‐FL:

WAIT FOR INITIALIZATION TO COMPLETE

SHUTDOWN SEQUENCE

1. Close VS‐ASW‐FL software

2. Shut down computer FIRST

3. Turn off Controller (BX‐UCB)

4. Turn off IX2‐FCB

5. Turn off X‐Cite lamp

6. Transfer data to external drive and delete

from computer

______________________________________________________________________________________________________________________________________________

MAKE SURE YOUR SLIDES ARE CLEAN (TOP & BOTTOM) BEFORE LOADING DO NOT LOAD SLIDES DURING SOFTWARE INITIALIZATION

CONTENTS

BRIGHTFIELD (BF) slide scanning – SINGLE Slide .......................................................................................... 2

FLUORESCENCE (FL) slide scanning – SINGLE Slide .......................................................................................... 4

BRIGHTFIELD (BF) slide scanning – BATCH Scans ............................................................................................ 6

FLUORESCENCE (FL) slide scanning – BATCH Scans ......................................................................................... 8

Troubleshooting .......................................................................................................................................... 10

FILTER SPECS

Single band (Move XY before switching channels)

DAPI‐FITC‐TRITC‐Alx647

Excitation (nm) Emmision (nm)

DAPI 375/28 460/50

FITC 480/30 535/40

TRITC 540/25 605/55

Alx647 638/31 694/60

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BRIGHTFIELD (BF) slide scanning – SINGLE Slide 1)

a. For first time users, click on the “Scan Projects” tab and choose ‘VS110 – Brightfield’ project. This

will populate the parameters with the most common settings (20x detailed scan, VSI file format).

You can modify settings during the scan setup.

b. For all other users, you may apply your own Scan Project as above or click on:

under Single Slide Scan column.

2) Click on ‘Load/Unload Slides’ button to put stage in loading position and carefully load slides. Ensure

slides sit flat and un‐tilted on stage. Click ‘Load/Unload Slides’ button when complete.

3) Fill out ‘Slide Properties’ left column as needed.

4) Set naming and saving parameters in ‘Automatic Naming and Saving’ middle column.

5) Click ‘Overview’

6) Once overview image is completed, choose objective magnification for detailed scan. ‘Z‐Scan Mode’

should be set to ‘Scan one Z‐plane’. If you require more than one Z‐plane, please see a member of

staff.

7) Click ‘Edit Scan Area’

8) Under ‘Scan Area’ in the left column. You can either click on ‘Create Scan Area’ button to allow

the program to automatically detect and draw Scan Regions around your samples or you can choose

`Remove All Scan Areas` to draw your own. Use mouse wheel to zoom.

9) Under ‘Detailed Scan Settings’, make sure ‘Scan whole area and focus sample only’ (middle button)

option is selected.

10) Next, click on to put down a focus map. Choose the Focus Grid Density in the left

column. You can manually add more Focus points with a mouse click, move existing focus points or

select and delete those not required. NOTE: The more focus points you put down the longer the scan

will take. Flat (fold and bubble free) samples with good contrast do not need a large amount of focus

points while samples with less contrast and/or uneven surfaces require more points.

11) When done click on

12) If ready to proceed, click on ‘Scan Now’. If you require more focusing options, click on ‘Next’

a. In the ‘Focus Settings’ menu, you may choose the Focus Logic. Options are Automatic

(Default), Semi‐Automatic (user confirms automatic focusing at each point) and Manual (user

manually sets each focus point).

b. You can now click on the ‘Scan Now’ button.

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13) Once completed you have several options:

a. You may Add another Detailed Scan to the existing slide

b. Scan a new slide with the current parameters

c. Remove/Unload current slide

d. Save Project (HIGHLY RECOMMENDED*)

e. Or finish the experiment.

*To preserve your scan parameters, it is highly recommended that you Save your Project so you do not

have to worry about accidentally using a previous users settings.

14) If not saving a project, Click ‘Finish’ and save your scans if you have not done so.

15) To remove the slide, click on and choose ‘Load/Unload Slides’.

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FLUORESCENCE (FL) slide scanning – SINGLE Slide 1)

a. For first time users, click on the “Scan Projects” tab and choose ‘VS110 – Fluorescence’ to populate

the parameters with the most common settings (20x detailed scan, VSI file format, typical

exposure etc.). You can modify settings during the scan setup.

b. For all other users, you may apply your own Scan Project as above or click on:

under Single Slide Scan column.

2) Click on ‘Load/Unload Slides’ button to put stage in loading position and carefully load slides. Ensure slides

sit flat and un‐tilted on stage. Click ‘Load/Unload Slides’ button when complete.

3) Fill out ‘Slide Properties’ left column as needed.

4) Set naming and saving parameters in ‘Automatic Naming and Saving’ middle column.

5) Click ‘Next’

6) Under ‘Overview Type’, choose the method you want to collect your overview.

a. BF (Brightfield): Quickest method but only if your sample has enough contrast. Click drop down

arrow ↓ to choose Normal, Dim or Faint Sample to correspond to level of contrast.

b. Tissue: To scan a fluorescence overview image on tissue samples. Click drop down arrow ↓ to

choose filter set.

c. Cells: To scan a fluorescence overview image on tissue samples. Click drop down arrow ↓ to

choose filter set.

7) Choose objective lens for overview image (2x is usually sufficient).

8) If you chose option (a) or (b) above, click ‘Start Live’ button under ‘Exposure Time’ column to set exposure.

Use joystick to navigate to sample.

9) Click ‘Overview’ button.

10) Once overview image is completed, choose objective magnification for detailed scan. ‘Z‐Scan Mode’ should

be set to ‘Scan one Z‐plane’. If you require more than one Z‐plane, please see a member of staff. Click

‘Next’ button.

11) Click ‘Edit Scan Area’

12) Under ‘Scan Area’ in the left column. You can either click on ‘Create Scan Area’ button to allow the

program to automatically detect and draw Scan Regions around your samples or you can choose `Remove

All Scan Areas` to draw your own. Use mouse wheel to zoom.

13) Under ‘Detailed Scan Settings’, make sure ‘Scan whole area and focus sample only’ (middle button) option

is selected.

14) Next, click on to put down a focus map. Choose the Focus Grid Density in the left column.

You can manually add more Focus points with a mouse click, move existing focus points or select and

delete those not required. NOTE: The more focus points you put down the longer the scan will take. Flat

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(fold and bubble free) samples with good contrast do not need a large amount of focus points while

samples with less contrast and/or uneven surfaces require more points.


16) If you chose one of the preset Scan Projects, the list of filters under ‘Channel Settings’ should be filled with

the default choices. Otherwise, to add a channel, click and choose to add a single or multiband filter

set. To remove a channel, click .

17) Select Channel 1 (this is the channel that will be used for focusing so it should be your brightest and most

widespread) and click

18) In the Stage Navigator window in the far right, make sure the yellow square is in the middle of your

Detailed Scan area. If not, click inside your region of interest to move the stage.

19) Refer to the histogram in the top right window. Change the Exposure Time so that you achieve at least

1000 counts in the mean intensity reading.

The XM10 fluorescence camera is a 14‐bit camera, allowing for a high dynamic range (16384 bit depth). It

is recommended to use as much of this range as possible (without excessive exposure times causing

photo‐bleaching) to capture as much data as possible for potential post‐scan analyses.

20) If ready to proceed, click on ‘Scan Now’. If you require more focusing options, click on ‘Next’

21) In the ‘Focus Settings’ menu, you may choose the Focus Logic. Options are Automatic (Default), Semi‐

Automatic (user confirms automatic focusing at each point) and Manual (user manually sets each focus

point).

22) You can now click on the ‘Scan Now’.

23) Once completed you have several options:

a. You may Add another Detailed Scan to the existing slide

b. Scan a new slide with the current parameters

c. Remove/Unload current slide

d. Save Project (HIGHLY RECOMMENDED*)

e. Or finish the experiment.

*To preserve your scan parameters, it is highly recommended that you Save your Project so you do not

have to worry about accidentally using a previous users settings.

24) If not saving a project, Click ‘Finish’ and save your scans if you have not done so.

25) To remove the slide, click on and choose ‘Load/Unload Slides’.

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BRIGHTFIELD (BF) slide scanning – BATCH Scans 1) Carefully load slides onto the stage. The stage positions are numbered #1 to #5, left to right. If you

need more room load slides, use the joystick to move the stage.

2) To scan multiple brightfield slides, click on: under Batch Scan column.

3) Highlight each slide and fill out its properties in the appropriate rows and columns. Then click ‘Next’

when done. A template can be used to pre‐fill these properties. Talk to staff if needed.

4) Under the ‘Slide Loader’ column, you are now able to load one or more previously saved Scan

Project(s) or use the provided ‘VS110 – Brightfield’ project for typical parameters.

5) In the ‘Scan Settings’ column and ‘Magnification and Image Document’ tab, select desired

magnification and Z‐scan mode.

6) a) Click the ‘Apply settings to all slides’ button to save these settings to every slide in every

cassette. All slides in the loader should now be highlighted green if 20x lens is used (10x is labelled

yellow while 40x is labeled blue).

b) If you only want to scan a selection of your slides, hold the Ctrl‐key and click the positions in the

cassette to select only the slides you wish to scan. Once the selection is complete, repeat step 5) and

click the ‘Apply settings to selection’ button to save settings to just the selected slides. The

selected slides in the loader should now be highlighted green (or otherwise).

c) If you want to scan different slide selections with different parameters/projects, repeat steps 4 – 6

for each slide selection.

7) Set naming and saving parameters in ‘Automatic Naming and Saving’ column and click ‘Overview’.

8) If for whatever reason you need to scan a single slide NOT loaded in the cassettes, click on ‘Priority

Scan’ to interrupt the batch process.

9) Once overviews are completed, you can review each slide in the ‘Batch Slide Selection’ column. With a

slide selected, click on ‘Edit Scan Area’ button.





option is selected.



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14) Select next slide in the ‘Batch Slide Selection’ column and repeat steps 10 – 14.

15) If you do not wish to scan a particular slide(s) in the batch, select the slides in the list and click on

‘Exclude slides from the batch scan’ button to exclude from batch scan.

16) If ready to proceed, click on ‘Scan Now’.

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FLUORESCENCE (FL) slide scanning – BATCH Scans 1) Carefully load slides onto the stage. The stage positions are numbered #1 to #5, left to right. If you

need more room load slides, use the joystick to move the stage.

2) To scan multiple fluorescence slides, click on: under Batch Scan column.

3) Highlight each slide and fill out its properties in the appropriate rows and columns. Then click ‘Next’

when done. A template can be used to pre‐fill these properties. Talk to staff if needed.

4) Under the ‘Slide Loader’ column, you are now able to load one or more previously saved Scan

Project(s) or use the provided ‘VS110 – Brightfield’ project for typical parameters.

5) In the ‘Scan Settings’ column and ‘Magnification and Image Document’ tab, select desired

magnification and Z‐scan mode. You may also modify the ‘Overview Settings’, ‘Illumination Settings’

and ‘Focus Settings’ tabs. However, you will have a chance to modify these settings later.

6) a) Click the ‘Apply settings to all slides of all cassettes’ button to save these settings to every

slide in every cassette. All slides in the loader should now be highlighted green if 20x lens is used (10x

is labelled yellow while 40x is labeled blue)..

b) If you only want to scan a selection of your slides, hold the Ctrl‐key and click the positions in the

cassette to select only the slides you wish to scan. Once the selection is complete, repeat step 5) and

click the ‘Apply settings to selection’ button to save settings to just the selected slides. The

selected slides in the loader should now be highlighted green (or otherwise).

c) If you want to scan different slide selections with different parameters/projects, repeat steps 4 – 6

for each slide selection.

7) Set naming and saving parameters in ‘Automatic Naming and Saving’ column and click ‘Overview’.

8) Once overviews are completed, you can review each slide in the ‘Batch Slide Selection’ column. With a

slide selected, click on ‘Edit Scan Area’ button.





option is selected.




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13) Select next slide in the ‘Batch Slide Selection’ column and repeat steps 10 – 14.

14) In the ‘Scan Settings’ column, set the parameters required for the ‘Magnification and Image

Document’ tab, ‘Illumination Settings’ tab and ‘Focus Settings’ tab if required.

15) If you do not wish to scan a particular slide(s) in the batch, select the slides in the list and click on

‘Exclude slides from the batch scan’ button to exclude from batch scan.

16) If ready to proceed, click on ‘Scan Now’.

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Troubleshooting Sample not recognized

For weakly stained samples with poor contrast (for example, brightfield slides with weakly staining dyes, very

sparse stained areas OR brightfield overviews of fluorescently stained samples).

During the editing scans dialog you will see the following settings in the left column:

Figure 1.

To increase the threshold of sample detection, modify the Sample detection sensitivity slider. In the example

below (Figure 2) with the slider at ‘0’, you see only a small percentage of the spinal cord tissue sections

detected by the system as indicated by the white, highlighted background. With the slider set to +10 (Figure 3),

almost all the sections are highlighted. Sample detection is also important when creating focus maps on scan

areas. Under ‘Detailed Scan Settings’, if the ‘Scan and focus sample only’ or ‘Scan whole area and focus sample

only’ (first and second button from left) is selected. Focus maps will only be placed on

samples that have been detected (as described above). If your sample is still too faint to be detected, you will

have to choose the 3rd button ‘Scan and focus whole area’ after manually drawing the scan area and/or

manually add focus points.

There are various options in the ‘Sample Detection Settings’ and ‘Advanced Sample Detection Settings’ menu

to assist in fine tuning detection of your samples.

When your samples are successfully highlighted, you can now click the ‘Create Scan Area’ button

which will automatically put a scan area around the detected sections (Figure 4). This is especially useful if you

have many sections on the one slide to avoid manually drawing scan areas.

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Figure 2. Brightfield overview image of fluorescently stained mouse spinal cord cross sections, sample

detection sensitivity set to Zero.

Figure 3. As above with sample detection sensitivity set to +10.

Figure 4. As above after clicking on ‘Create Sample Area’ button.

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If you choose Brightfield overview scan for your fluorescent sample, there are various options in the drop

down arrow menu. Choosing BF (brightfield) you have a choice of Normal, Dim and Faint samples.

Depending on the choice, the program will manipulate the brightness and gamma to improve the contrast of

the samples on your slide, giving you a greater chance of sample detection (mentioned above).

BF – Normal Samples

BF – Dim Samples

BF – Faint Samples

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Focusing Issues

After setting focus maps on your samples and clicking ‘Scan Now’, the system will go to each focus point to set

the focus. If the focus is found, the focus point square will change colour to green. If the focus could not be

found, the focus point square will change to grey. The scan will proceed if there is at least ONE green focus

point square.

Various focusing issues and possible solutions:

1. Samples are weakly stained (either brightfield or fluorescent).

o In the case of weakly stained brightfield samples, go into ‘Live’ mode before proceeding with

the scan to manually set exposure times.

o In the case of weak fluorescent signals, increase the exposure time of the focusing channel

(channel on the top of the list) so the mean intensity on the histogram is at least 1500 counts

(Page 5). Always choose the strongest and most widespread fluorescent channel to be the

focusing channel.

2. Samples are too thick or too thin.

o Thin samples <5 microns will have a smaller volume of fluorescent signal. Ensure that the stage

is close to the focus by going into ‘Live’ mode before proceeding with the scan.

o Thick samples >50 microns will have many points of focus. The algorithm will usually choose

the top of the sample.

3. Stage is too far away from sample or focusing algorithm gets ‘lost’.

o Pertaining to both points 1 and 2, double check in ‘Live’ mode to make sure the stage is at

least close to the focus of your sample.

o Avoid putting focus maps on empty areas where there is no sample. Focus maps on a glass

slide can often bring the stage far from the focus.

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