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Digital Slide scanners: A basic approach to scanning slides and scanning infrastructure

Digital Pathology is a field focused in generating data from digitized specimen scanned slides, sometimes referred to as whole slide imaging (WSI), a succession from traditional microscopy. In its full potential, it is anticipated the further use and development of digital pathology equipment and infrastructure will allow data/information to be transferred across large distances quickly. As you consider your purchase for a slide scanning system, you may find yourself wondering how to use a slide scanner. This blog will go over some of the basic steps to use a slide scanning system

The slide scanning process consists of the following steps

1. Preparation of glass slides

2. Placing slides in the glass slide racks

3. Unlocking and opening of the scanner door

4. Placing glass slide racks in the rack store

5. Closing the scanner door

Let’s go over the process in detail:

To prepare glass slides for scanning we must use only compatible glass slides that fit the glass slide rack. Other important precautions include the following:

  • Make sure that the cover glass does not protrude over the edge of any portion of the glass slide

  • Make sure label is positioned flat on the glass slide and does not extend over the slide edge

  • Follow your laboratory instructions to prepare the tissue for mounting, staining and applying a coverslip

  • To prevent tissue from being excluded from scanning, place the tissue under the cover glass >5 mm from slide label and >3mm from coverslip edge

  • A minimum of 15% of the slide surface must be left empty (no tissue), as the scanner requires this as a reference in order to correctly detect the tissue

  • Make sure that the tissue area of the glass slide is clean of markers, scratches, dirt on or under the cover glass

In order to efficiently scan slides it is important to focus on image quality and ensure quality control. Your scanner usually comes with a quality control protocol and following that will ensure the seamless functioning of your scanner. For example, no wet or freshly made slides with glue or mounting media should be present outside of the coverslip. The coverslip and label must be placed properly. The slides should be cleaned before each scan .This will help prevent dust buildup and reduce scan time. Simple steps like keeping a notebook close to scanner to document scanner errors may be helpful.

Now let us discuss the factors affecting the image quality obtained in your scanner. The image quality of the obtained image depends on the quality of the tissue preparation. Therefore, you need to make sure that the glass slide is clean and does not contain scratches on the tissue area. Also, ensure that the tissue is not too thick or too thin. Lastly, make sure that the tissue is not folded, over or under-stained.

Another important aspect of scanning is the orientation of your slide labels. Make sure the barcode orientation ls either vertical or horizontal and firmly affixed to the glass slide. Avoid dirt, pen marks, bleaching, staining and scratches on code area. Affix the code label only on the upper side of the glass slide and ensure the label does not run on top of the coverslip. Do not use oversized or undersized labels. Use only one code label on one slide. Do not use folded labels or place a new label on top of another label.

Of note, while operating a scanner, glass slide racks must be prepared outside the slide storage. Adding, replacing, or removing single slides to or from a rack inside the slide storage, can lead to skipping of slides and system errors. Incorrectly positioned glass slides can lead to serious damage and may cause an obstruction inside the slide storage and prevent movement of the slide handler. One must make sure that slides are not sticking out of the slide storage. This may cause the handler to collide with slides. When loading or unloading glass slide racks to or from slide storage watch for sharp edges of slides. Putting back an already scanned slide rack will result in rescanning all glass slides present in the glass slide rack.

Understanding the functioning of a slide scanner is not complete without emphasizing the role of trained personnel. An investment in personnel is important for the efficient use of the slide scanner and for data management. In most cases, the vendor will install the machinery and then train 1-2 personnel on staff for the hardware/software aspects of the slide scanner. These 1-2 personnel are then “primary users” who should commit their efforts into developing standard operating protocols, carrying out operations (i.e. slide loading, slide scanning, and general software set-up) and finally exporting/managing data. There is also the topic of data management, and without dedicated personnel this can cause disarray of what has been scanned in. Institutional personnel (such as those in IT) should also be involved in conversations regarding slide scanner purchases as they may be needed to advise on optimal network connectivity for data input/output from onsite or approved offsite.

We hope that this introduction to the usage of slide scanners will be helpful to all those who are looking to use digital pathology as a tool in pathology. As always, all feedback is welcome! Happy reading!


1. Digital Pathology Association: College of American Pathologists Digital Pathology Topic Center:

2. National Alzheimer’s Coordinating Center (NACC):

Blog Author

Nupur Sharma, MD

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