Visiopharm: FAQs - Software

Make sure that the label transparency slider is not at 100% in the label properties dialog.

Also make sure that you are viewing the active field of view - yellow rectangle, if you are working with a DP version.

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The labels on my classified images are a different color than when I last reviewed them.

If you load a different protocol than the one used to classified the images, the properties for the labels could be different. If you load the original configuration in Visiomorph, the labels should change back to the color you originally chose in your configuration.

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How do I delete part of a mask/label?

First of all you need to have the proper tool active. To delete (part of) a mask, open the mask tool and choose the Clear mask. Cover the area of the mask that you want deleted with the clear mask. After double clicking to finish the clear mask, the mask that you covered will be changed.

To delete a label (or part of) open the label tool and choose the Clear label. This can now be used as an eraser by moving it over the label you want to remove (click and hold mouse).

To undo/redo step-wise in either mask or label, open the corresponding tool and use the undo-redo buttons or use backspace/space on the keyboard. Note: This only works for masks as long as you have not double clicked to finish it. Undoing a mask after is finished will remove the whole mask.

Tip: the undo button in the label tool is also used to go back and forth between classification and training in Visiomorph.

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When I draw a mask on a sample image in Visiomorph, the mask disappears when I double click to finish it

Note that all images that come from a sampling step in Acquisition will have a mask (Mask001 as default) around the edge of the image. If you use the same mask to outline a region as the one that is already covering the image, the new mask will be included in the existing and therefore not saved as a separate mask. Use a different mask to outline the region, or start by changing mask001 to the clear mask before outlining your ROI.

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How do I view the properties for the labels and masks in my image

To see the "pop-up pane" with label area, irregularity etc. when you hold the mouse cursor over the label, the label tool has to be active and the labels, which you want to see the properties for, must be inside a mask (they cannot be in clear mask area). Furthermore the mouse cursor should be 4-armed to indicate that the area is active.

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When I am doing counts in newCAST I cannot get it to save the data on the right level in the database.

When you start counting in a new study, you always have to start by pressing the 'new datasheet' button on the toolbar, before starting the count. You can then log the counts to the database level you are at during the counting session. Remember to also start at new sheet whenever you start counting in something that should be saved in another place in the database.

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I have recalibrated my lenses but my Super Images in newCAST still do not look right.

I have recalibrated my lenses but my Super Images in newCAST still do not look right.

When you have done the calibration in Acquisition, saved the configuration and shift to the newCAST module, you need to open the newCAST acquisition properties and load the configuration that you just created/saved in order to load the correct calibration of lenses.

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Nothing happens when I try to start a sampling in one of the autosampler modules (MicroImager, ArrayImager, Section Assembler)

The sampling cannot begin before you have turned on the live view (play button below camera).

Note: When you are using different kinds of virtual slides, remember to set up your lenses with a slide from the correct scanner type (Aperio, Hamamatsu, Olympus, etc.)

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I get an error message from MicroImager that my lenses have changed. What should I do?

Go to the Acquisition properties - camera setup and setup lenses using the same type of virtual slide file as the images you have in your Super Image list.

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How do I apply a Visiomorph configuration to more images at once?

Mark the images in the database that you want to process. If you want to process an entire study/study unit, just mark the study/study unit name. Otherwise use crtl+click to mark the images you want processed.

Then click the batch process button on the toolbar:

This opens the batch process dialog. You can check/uncheck what levels should be processed, depending on whether your images are on Measurement or Details level (or both). This also gives you the option to create a report from the batch process.

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When I preview a feature image in Visiomorph it is either all black or all white.

Open the display properties (small color pallet button on the toolbar or shift+right click in image) and set Stretch to Minimum to Maximum (do not set it to individual on colors).

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How do I import images in to VIS?

You can only import from the View/Multi View/Visiomorph/newCAST modules. When you are in one of these modules, you can go to File - Import - Images. Make sure to choose the right template to import the images so that the database entry names correspond to the correct folders.

Remember to specify the format of the images you want to import.

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When I try to open my WS/virtual slide file I get an error

Make sure you have the corresponding viewer installed. To view Scanscope virtual slides files you need to have Imagescope installed on the computer, for Hamamatsu .ndp files you need NDP-view and for Zeiss mirax images you need the the Mirax viewer.

Make sure that the WS file is still located at the path you imported it from. Moving the WS file after importing will prevent the program from opening it, before you either move it back or re-import it.

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The mask on my Super Image in the Navigator or MicroImager does not match the one on my live view.

Make sure that 'Discard resolution' is not checked in the preferences dialog under Image resolution:

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Excel view button is not active ("grayed out" on the toolbar)

You need to install Office web components (owc11) and the necessary updates. If owc11 is not installed it can be downloaded from:
www.microsoft.com/downloads/details.aspx?FamilyId=7287252C-402E-4F72-97A5-E0FD290D4B76&displaylang=en
You also need two updates, SP1 and KB947318 which can be downloaded from
www.microsoft.com/downloads/details.aspx?familyid=C815DFFA-D5F3-4B71-BF46-13721BD44682&displaylang=en
and
www.microsoft.com/downloads/details.aspx?familyid=644008E0-77C9-4A02-AC9B-E30D0930C4BE&displaylang=en

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The VIS icon (shortcut) on my desktop will not start the program until the MSI package has been located.

This can be because the shortcuts in Windows 7 have been removed. Try to restore them.

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VIS asks to resample when I start a complete scan or I get an error

There is limitation both from the VIS program, the virtual slide viewer programs and your PC on how large images in can work with and store. If you are trying to scan a large ROI at a high magnification it could become too large to handle. The image cannot exceed 100MB and this means that the size of the resulting image (from the complete scan) should fulfill the condition

Pixels_X are the number of pixels in the x-direction and PixelsY are the number of pixels in the y-direction.

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The Section Assembler auto-align does not seem to work. What should I do?

Check that the align parameters are set correctly. If you use tissue detect you can utilize this in the alignment by choosing labels as a parameter. If not, make sure to choose image as alignment parameter and not labels.

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