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Digital Microscopy


PathXL facilitates digital microscopy by offering slides online. The slides are scanned, uploaded, and offered to students by way of a URL. A microscope is no longer required to view the slides, which can now be accessed from any computer at UU or at home.

This allows students to prepare for practicals at home, perform practicals from home entirely by digital means, and/or review slides at their leisure. Teachers are no longer tied to practical rooms with available microscopes or to limited numbers of physical slides.

Take a look at an example of a digital slide.


PathXL offers numerous ways to use digitised slides in education:

  • Students can use PathXL to prepare for a practical, reducing the need for instruction during the practical.
  • Students can (be instructed to) take a second look at the slides they worked with in the practical in their own time.
  • Practicals can be conducted from a computer rather than from a microscope. Everyone will be looking at the same slide, making it easier for groups of students to examine and analyse structures together.
  • A practical can be replaced entirely by an e-learning module which students can complete through self-study. Reviewing digital slides will be an integral part of such an e-module. Take a look at this example of how PathXL has been implemented in Xerte.

Scanning, uploading, and providing access to the slides is handled by the CPIO (Biology, cpio@uu.nl). Teachers are assigned an account in PathXL which allows them to add their own notes to the slides. Please follow these steps to get you started with PathXL:

  1. Send an e-mail to cpio@uu.nl in which you state which coupes you want to use.

If the coupes need to be scanned, start no later than three weeks prior to the start of the course. If you want to use existing material in PathX, then start no later than one week prior to the start of the course.

  1. Analog coupes can be scanned. Make an appointment with CPIO. After about a week, your analog coupes will be published online. For each coupe, indicate the subject, colors, and owner.
  2. You will be granted access to the server with relevant material to select digitalised coupes.
  3. Now book an appointment for instruction about PathXL with CPIO. This can be done simultaneously whilst collecting the scanned coupes.
  4. Optional: follow a workshop on PathXL.
  5. Create cases in PathXL on the coupes. These cases receive a unique URL which you can use in your education. One cases can contain multiple coupes.
  6. You can now also make annotation in coupes.
  7. The URLs can be shared with your students through BlackBoard. Students do not need to log-in once they received the link.


Starting date: semester 1 2015-2016. This tool is licensed infinitely.

  1. How do I digitise my slides (or have them digitised)?

The slides are scanned at the Pathology department of the UMC. You can submit your slides to the CPIO (cpio@uu.nl, Kruytgebouw Z406). They will usually be scanned and become available online within a week. The CPIO will require you to submit some additional information (metadata) about the slides so that they can be properly stored and organised.

  1. What requirements do slides have to meet?

Most slides are already old enough that they will need to be scanned by hand. Their dimensions will be off, or the preparation will have lost too much colour to allow for automatic scanning. It may be helpful to put a new piece of cover glass on the slide if the light got to it.

  1. At what magnification and are the slides scanned, and what options will the student have when viewing them?
  • A standard scan is performed at 40x magnification, at a resolution of 0.2 to 0.5 microns per pixel (resulting in an image of about 20,000 by 20,000 pixels). The student can zoom into and move around the image.
  • It is also possible to scan multiple layers (Z-stack). This will allow students to quickly switch between layers, looking deeper into the slide. Bear in mind that each additional layer will increase the file size. If you want multiple layers of your slides scanned, please specify the number of layers and each layer’s depth.
  • Fluorescent slides can also be scanned. The different colour channels will be viewable separately.
  • Students can rotate the image, measure distances and surface areas, and compare slides side by side.
  • Students can also view the slide’s label, though unfortunately the labels on old slides are often illegible or only partially scanned.
  • The teacher can add notes, arrows, circles, and explanations to digital slides, which can help students make the most of a slide.

Digital or virtual microscopy practicals let students practice regardless of timeframe or location. This means they are better prepared for the traditional practical, where coaching is available for acquiring the required skills. With Path XL digital practicals, students can cooperate more easily and work on more similar slides, which facilitates feedback and plenary discussions. What’s more, it makes rare and fragile slides available to everyone.

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