Visiopharm: FAQs - Hardware

Visiopharm has the following recommendations:
For stereology: PC with specifications corresponding to
DELL PC model T3500 525W Intel Xeon W3550 (3.06GHz,4.8GT/s, 8MB, 4 cores) with 500 GB HD, 4096 MB RAM, Dual monitors (resolution 1600x1200, 20"), 16X DVD+/-RW Drive, 2 serial ports, 256MB nVIDIA Quadro NVS 290 DVI/VGA output graphic card.

For Whole Slide analysis: PC with specifications corresponding to
DELL PC model T3500 525W Intel X5650 (2.66GHz,6.4GT/s,12MB, 6 cores) with 1,5 TB HD, 4096 MB RAM, Dual monitors (resolution 1600x1200, 20"), 16X DVD+/-RW Drive, 2 serial ports, 256MB nVIDIA Quadro NVS 290 DVI/VGA output graphic card.

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VIS freezes after a while during live view with an Olympus DP71 camera. What should I do to resolve this matter?

First of all check if the hardware shares interrupt request number (IRQ) with other hardware. This is done by using the Device Manager found in: Control Panel - System - Hardware - Device Manager. In here choose View - Resources by type. Click the plus sign in front of Interrupt request (IRQ). The number mentioned after the card name is the IRQ number, for example (ISA) 12 Dell Touchpad.

Unfortunately it is not easy to make sure that there is no conflict of IRQs. The best solution is to switch PCI cards around and run diagnostics until the best setup is found.

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My DP72 camera is connected and I can see it in the device manager but I still get a black image.

The DP72 camera has an extra power cord connected to the PCI card. Check that this is correctly attached so that the camera card has a full power supply. Check that the camera has the correct driver. Go into the Device Manager and find MalAd Device. In driver version it should say: 4.1.4.1

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When I take an overview (Super) Image, it is not stitched together correctly.

There are a number of things that can influence the quality of the stitched images

Camera rotation

To check if the camera is rotated, insert a calibration slide or another slide with lines that are guaranteed horizontal. Go to a high magnification (>20X) and align horizontal grid lines with top/bottom of the field of view. If they are aligned, the camera rotation is fine, if not, loosen the camera screws and fix the rotation so that grid and field of view is aligned. Note that the camera will move a little bit when the screws are tightened again.

Lens calibration

You can check if the lens calibration is OK by inserting a calibration grid and use the measure tool to see if it measures correct. One square in the calibration grid is 10um and the whole cross on the slide is 2000um.

If the calibration is not correct, calibrate your lenses by following the procedure described in the help (F1) under lens calibration.

Important: make sure that the unit (set this under measure properties, F2) is in um, since this is the unit for the calibration slide. Otherwise your calibration will be incorrect.

If both camera rotation and lens calibration is correct, check that the setting 'discard resolution' is not checked under Preferences - Image viewing.

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My stage is making strange noises

There are 5 main reasons why a system makes noise:

The noise is normal, most motors will make some noise. This would be in the form of a whirring sound as they move and in some cases a crack or high pitched tone.

The noise is generated by the combination of the drive electronics and the type of motor on the equipment.

The noise has become louder and your system is no longer performing correctly.

This is likely to be the motor stalling, i.e., failing to move due to resistance.

Check for any obstructions, such as screws, shards from glass slides, or metal shaving which may be impeding the movement of the equipment.

Should the controller of the system not have standard acceleration and speed settings, please reset the controller to original settings. Ask the stage manufacturer for further details

My stage makes whining noise and does not move to the correct position.

This is likely to be the motor stalling, i.e., failing to move due to resistance.

Check for any obstructions, such as screws, shards of glass slide, or metal shaving which may be impeding the movement of the equipment.

My stage makes a grinding noise when it moves.

Check for any obstructions, such as screws, shards of glass slide, or metal shaving which may be impeding the movement of the equipment.

The noise is different from normal (or other axis) and my equipment does not always perform correctly.

This is most likely to be a faulty drive module.

Please follow the drive module investigation instructions to identify the faulty module.

Report this to Visiopharm support.

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My stage moves too far in the X- or Y-direction so that my objectives come too close to the stage edges.

To make sure that the stage does not travel too far you need to set the limit switches for the stage.

There are two limit switches on both the X and Y axis that is used to set the limitation of the stage movement and these can be changed manually.

Most modern stages have adjustable limits; these are protected by the drive covers. Use limit changing to change the limits on your stage.

Make sure when setting the limit switches that you check for any obstructions, such as condenser lens, objectives or microscope frame to see if any of these components are impeding the movement of the stage.

For further help on setting the limit switches for your stage please contact Visiopharm Support

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There is an uneven light on my images.

Make sure that the condenser is at the position it should be for the given lens (in for high magnification/out for low magnification).

If the condenser is at the right position, try to adjust the Köhler illumination:

1)  Remove all filters, prisms and Phase rings. The microscope is now setup for Bright field microscopy.

2)  Select an objective, normally 10X. Magnifications below 10X are not to be used.

3)  Focus on a specimen using the microscope focus drive.

4)  If using a lamp house where the collector lens and lamp can be adjusted, the correct distance in between is found where the best possible and homogeneous illumination of the field of view is seen. Note. Most microscopes do not offer this feature.

5)  Close Field Diaphragm until it is visible in the field of view.

6)  The transition between the Field Diaphragm and the specimen needs to be as sharp as possible, this is adjusted using the condenser drive on the microscope

7)  If the Field Diaphragm is not in the center of the field of view, use the condenser centering screws to adjust.

8)  The Field Diaphragm is opened until it just disappears from the field of view. Make sure not to open it completely as this will allow stray light in the system. Thus lowering the contrast and creating a blurry image.

9)  In order to adjust the aperture diaphragm correct, one of the eyepieces must be removed. When looking down the empty tube on the tubus the intermediate image plane can be seen. In this focal plane the aperture diaphragm can be seen. At the correct setting, 2/3 to 1/1 of the field of view is covered by the diaphragm .

10)  Replace the Eyepiece. The microscope is now adjusted according to the Köhler principle.

11)  This procedure should in principle be followed every time you change objectives, especially when taking pictures. In praxis a 10X or 20X objective is used for the adjustment and the setting is then used for the higher magnifications as well.

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When I am doing a sampling in acquisition or newCAST mode, my stage seems to move too fast and 'jumps' out of position so that the sample image position is off relative to the position on the Super Image.

Check the stage settings under Acquisition properties - peripherals - stage. Open the stage properties and check the settings for the speed and acceleration in the X/Y-direction. With settings of ~80-90% for speed and ~90-95% for acceleration, the stage should move correctly.

If lowering the speed/acceleration does not work, you can check that:

There is not dirt/dust in the spindle of the motor, creating extra resistance.

That the stage is correctly calibrated (if the stage has been in one of the limit switches, it needs to be re-calibrated). This is only valid for Ludl or Marzhäuser stages and VIS will automatically calibrate them when VIS is started and the live view is turned on.

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Not all my images are in focus when I take images of all slides in my 4- or 8-slide insert.

The stage insert need to be horizontally aligned. You can check if the alignment of the insert is acceptable by checking the z-axis value when you focus on slide, for one position at a time. It is a good idea to

Use the same slide for all positions

Use an empty slide with a line drawn on to make sure you always focus on the top of the slide.

Remember to check if there is any difference in both the X-and Y-direction.

If the stage alignment is acceptable, you can adjust the changes for the auto focus. These are set under Acquisition properties - Quality control - Auto focus. The 3 main parameters are:

Refocusing: How far can the stage travel before auto focus is performed?

Full focus search: Set the range where it should search for focus

Local Focus: Set the range where it should fine-tune the focus within. This is the parameter used during sampling.

Note that your choice of parameters can have a great influence on the sampling time. If you choose a wide range for the focus search or a small refocusing value, these will increase the sampling time.

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Auto focus is not working correctly. The result has a slight offset

It makes a difference on which side the focus motor is placed. If the focusing performs a little bit slow and with some offset, then try to reverse the direction of the process. Do this by adjusting the Full Focus Search: Z-axis range. It matter if it goes from negative to positive or the opposite. Try to do the opposite of what it has.

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