FAQs

You will find answers here for the more Frequently Asked Questions.

How do I register my copy of SmartType?

Download SmartType from our download page. When you run SmartType on your computer you will be presented with a splash screen.

At the bottom of the Splash screen there is a section that lists information that we will need to register SmartType on your computer. If you are on a computer which is configured with email, click on the info@dsuk.biz link and an email window will be created for you with the information already inserted. Simply add your name and company name and we will enable the full SmartType licence for your computer as soon as payment has been received.

If your computer is not configured to use email, cut and paste the information from the bottom of the Splash screen, transfer it to another computer and then email it to us.

How do I import a metaphase that is too large to fit into a single image?

Sometimes a metaphase is too large to be captured in a single field of view with the camera and the microscope magnification you are using, In this case you can create a larger image by capturing overlapping images with your capture system and then have SmartType stitch together the images into a single large image.

Simply select two or more images when importing the image and you will be presented with a dialogue that allows you to slide the images around relative to each other, Align the images, you do not have to be to careful, just get them near enough, and then click on the "Stitch" button to have SmartType align them perfectly and stitch them together.

Manually installing the Security.jar security file

When SmartType runs it collects information to determine the identity of your computer and then checks this against an encrypted security file to determine what features of SmartType should be enabled. SmartType will attempt to download the security file from our website. Sometimes due to networking issues the download may be blocked. In this situation, it is possible to download the security file from https://karyotyper.uk/Downloads/Security.jar and manually install it.

To manually install the security file follow these instructions:

1. Download Security.jar from the link above and save this file onto the computer running SmartType.

2. Run SmartType and select Install Security Key... from the Karyotype menu.

3. Select the Security.jar file in the dialogue that is presented and select Open.

What cameras can I use? What C-Mount do I need?

Problems importing metaphase images

SmartType can import images in either TIFF, JPEG or PNG format. Sometimes however, particularly with TIFF images, the image will fail to import. The reason for this is usually because an image saved in TIFF format can actually be stored in one of a multitude of different formats. Whilst SmartType does its best to work with a large range of possible TIFF formats, there are some formats that it does not recognise.

Usually, the problem can be solved by using another general purpose image processing application such as ImageJ to convert the image into a TIFF format that SmartType will recognise.

If you have not already got ImageJ, you can download it from the ImageJ Website

1. Start ImageJ

2. From the File menu select Open...

3. Select your original image file to open your image in ImageJ

4. Convert the image to a 8bit format by select 8bit from the Type sub menu of the Image menu

5. Save the converted image in TIFF format by selecting TIFF... from the Save As sub menu of the File menu

6. Nominate the name and location for the reformatted image file.

7. Quit ImageJ and from SmartType import the reformatted image file.

Where can I find some example metaphase images?

If you do not have any of your own metaphase images but are keen to see how easy it is to import metaphase images into SmartType you can download some example metaphase images from here:

Motic microscope configuration

Motic provide a very competitively priced high quality brightfield microscope that is well suited to karyotyping. We suggest the following configuration:

• Motic BA Elite 410 Series with sextuple nose piece

• Trinocular Head 20/80

• LED module (optional)

• Eye Pieces 10x22mm

• Green Interference filter (Important)

• Rackless Stage:

• Condenser:

• 0.5x C-mount

• 100x Planflour

• 40x Planflour (optional)

• 20x Planfour

• Moticam 5.0 (USB 5.0+) colour camera

How to Scale a Metaphase Image to the Optimum Size for SmartType

An ideal image resolution for SmartType is around 1300 by 1000 pixels. Modern digital cameras now often support resolutions much higher than this. In practice for Karyotyping this resolution add no extra value because the cameras have a pixel size smaller that the Nyquist limit for the given magnification (typically 100x) being used.

If in the SmartType Karyotype view, your the chromosomes appear considerably larger that the size of the ideograms then you will be getting less than optimum performance from SmartType.

The answer is either to capture your images at a lower resolution or scale your images after you have captured them to reduce the resolution.

Capture at a Lower Resolution

Many camera capture systems offer the ability to capture at lower resolution either by using a process called binning or by scaling  your image after capture. If available the details of how you do this will be in the User manual of your camera capture software.

If your camera has a resolution of around 2048 by 2048, try using a binning of 2 by 2 which will result in an image size of 1024 by 1024.

Scale Image Post Capture

If your capture software does not support the ability to create images of a suitable resolution, then you can use the free ImageJ software to do the scaling.

ImageJ is free to use software. You can download it from the ImageJ download page 

Once downloaded, run imageJ, Open your image, With the image open select 

• From the Image menu select Scale…

• Select Average when downsizing and Create new window

• Either fill in the desired Width or a suitable scale factor to create an image that is closer to 1300 by 1000

• Then select  Save As… Jpeg from the File menu to save the scaled image to your disk.

Improving G-banding image contrast

Green Filter

The Giemsa stain used for G-banding produces a light pink colour stain. The AT rich areas of the chromosomes bind with more of the stain and produce the darker pink bands.

The pink bands appear pink as they let more of the red portion of the light spectrum filter through to the eye or camera. For this reason G-banding contrast can be enhanced by blocking the red light at the source with the aid of a green pass filter. The result when seen by eye is that the image background appears green, but the dark chromosome bands appear black instead of pink.

In addition to enhancing the contrast of the pink stained chromosome bands there is a further benefit that in working restricted portion of the light spectrum (just the green wavelengths) you can make do with lower cost Semi-apochromatic or Fluorite objective lenses rather than the more expensive full Apochromatic lenses! So if you know your microscope is to be used just for G-banding karyotyping and not for full colour microscopy you can save quite a lot of money on the lenses!

Colour Cameras

Typically karyotype imaging has been carried out with monochrome (black and white) cameras. However, new high resolution good quality colour cameras can now be used and their resolution is sufficient that even if we just use the green channel for the camera we can get good quality G-band images. The advantage is that the colour camera can also be used for true colour brightfield imaging as well.

Annual licence vs unlimited licence

Importing MFISH images

BBC Interview with Prof. Darren Griffin - Dinosaur DNA

SmartType v3.4 TIFF with JPEG compression no longer supported

Since SmartType v3.4 TIFF files using JPEG compression (TIFF Encapsulated JPEG) are no longer supported.

If you try to import a metaphase image from a TIFF Encapsulated JPEG image you will see an error.

If you already have karyotype files that were created from TIFF Encapsulated JPEG these will not be able to be able to be opened in SmartType 3.4 and will have to be converted before they can be used.

Contact us if you encounter this problem as we can assist with that conversion.

The problem in more detail

TIFF is not a single file format but rather an open architecture means of organising image data. Whilst there are some versions of TIFF that are universally adopted other variants are either less common or even entirely proprietary. Using JPEG compression within a TIFF file is one of the less common formats. SmartType versions prior to 3.4 used a now obsolete image processing library. To help future-proof SmartType and SmartType karyotyper files it is important to avoid reliance on this technology.

JPEG images use compression that can reduce the size of a typical monochrome metaphase image by a factor 30 and the expense of a very minor loss of image quality. In practice, this moss of quality is immaterial to the needs of karyotyping. If you wish to retain the advantage of this image compression, it is advised that you switch to saving your metaphase images in JPEG format.

Security issues when openning SmartType on Apple Mac

If you open SmartType on an Apple Mac you may see a security warning dialogue saying that the app is not a registered app and so will not run. If this happens you can override your security settings and open SmartType by:

• In the Finder on your Mac, locate the SmartType application. Don’t use Launchpad to do this. Launchpad doesn’t allow you to access the shortcut menu.

• Control-click the app icon, then choose Open from the shortcut menu.

• Click Open.

SmartType will be marked as an exception to your security settings, and you can open it in the future by double-clicking it just as you can any registered app.