Digital pathology, defined
For most of its history, pathology has been practised at a microscope: a section of tissue is fixed, embedded, cut, stained, mounted on glass, and examined by eye. Digital pathology replaces the last step. The glass slide is scanned once, the resulting digital image is stored, and everything after that, from routine review through second opinions, teaching, archiving, and image analysis, happens on a screen.
The term covers the whole environment that makes that possible: the scanners, the whole slide images they produce, the storage and image management systems that hold them, the viewers that display them, and the analysis tools that work on them. It does not by itself imply artificial intelligence, although AI is the fastest-growing use of the images once they exist.
Three related terms are often used interchangeably and are worth separating. Whole slide imaging (WSI) is the scanning technology. Virtual microscopy is the act of viewing a scanned slide as if through a microscope, and is the phrase teaching programmes tend to use. Telepathology is remote pathology review, which digital slides make much easier but which existed before them.
How a glass slide becomes a whole slide image
- Scanning. A slide scanner moves the glass under a camera and objective, typically at 20x or 40x, capturing thousands of overlapping fields and stitching them into one image. Some scanners capture several focal planes (a Z-stack) so thick sections can be refocused later.
- Building the pyramid. The full-resolution image can exceed 100,000 pixels on a side and several gigabytes. The scanner therefore also writes progressively smaller copies (typically halving each level) and cuts every level into tiles. This multi-resolution pyramid is what makes the image usable: a viewer requests only the tiles for the region and zoom level on screen.
- Recording the scale. The file stores the physical size of one pixel in micrometres (often written as MPP, microns per pixel, around 0.25 µm at 40x and 0.5 µm at 20x). Every measurement in a viewer depends on this value.
- Attaching metadata. The label image, a macro overview, the scanner model, objective, and scan date travel inside the file, alongside any barcode the lab printed on the slide.
- Storing and serving. In a hospital, slides go into an image management system alongside the laboratory information system. In research and teaching, they usually sit on a file share, a cloud drive, or a laptop, and open in a desktop viewer.
Whole slide image formats by scanner vendor
There is no single digital pathology file format. Each manufacturer writes its own container, most of them variations on tiled TIFF, and the choice of viewer often comes down to which of these it can read.
Open-source libraries such as OpenSlide and Bio-Formats read most of these, which is why vendor-neutral viewers exist at all. SlideScope reads SVS, NDPI, VMS, VMU, MRXS, SCN, BIF, SVSLIDE, QPTIFF, AVS, DICOM, TIFF, and OME-TIFF; it does not read iSyntax or VSI. The file compatibility reference has the exact limits.
The software layers of digital pathology
People searching for "digital pathology software" usually mean one of five quite different things.
Scanner software
Controls the scanner and usually ships with a free viewer for that vendor's own format, such as Aperio ImageScope for SVS or Hamamatsu NDP.view2 for NDPI.
Image management systems
Hospital-grade platforms that store slides, connect to the laboratory information system, manage cases and worklists, and are validated for clinical use. Enterprise-priced and IT-deployed.
Desktop viewers
Applications that open whole slide images from a file, folder, or link on an ordinary computer, for review, measurement, annotation, and teaching. This is where SlideScope sits.
Analysis platforms
QuPath, CellProfiler, ImageJ and Fiji, ASAP, and commercial equivalents that segment tissue, count cells, and run scripted pipelines. A viewer typically hands regions to them as GeoJSON.
AI and computational pathology
Models that detect, classify, or grade tissue from the whole slide image. Some are cleared as clinical decision support; most are research tools that need the digital slide to exist first.
Research, teaching, and clinical use are different problems
Research pathology is where most slides get scanned today. A cohort is digitised once, reviewed by several people, measured, annotated, and fed into analysis. The requirements are vendor-neutral file support, calibrated measurement, annotations that survive a hand-off, and an easy way to send a collaborator the exact field of view. There is no regulatory gate; the tool just has to be accurate and fast.
Teaching uses digital slides as a virtual microscope. A course scans its slide box once and every student opens the same set on their own laptop, marks what they identified, and compares notes. This is why histology slide viewers that run locally on both Windows and macOS matter to universities.
Clinical primary diagnosis on a screen is regulated. Scanners and viewing systems used to sign out cases are cleared or approved as medical devices in most jurisdictions, laboratories validate them against glass, and displays are specified. General-purpose viewers, including SlideScope, are not cleared for this and say so. They are used clinically only for the non-diagnostic work around a case: teaching, conference preparation, research on archived material, and quality review where the institution's policy allows.
Benefits and limitations
What digital pathology makes easier: sharing a slide without shipping glass, reviewing the same region at the same time from different places, measuring reproducibly, keeping annotations with the image, building teaching sets that never fade or break, archiving without a slide room, and running image analysis or AI at all.
What it costs: a scanner, storage measured in terabytes, time to scan, a workflow to keep glass and digital in sync, and validation if the images will be used for diagnosis. Scanning also loses some things a microscope offers, such as refocusing through a thick section unless the scanner captured a Z-stack, and polarised light unless the scanner supports it.
Where SlideScope fits
SlideScope is a desktop digital pathology viewer for research, education, and review. It opens whole slide images from the major scanner vendors on Windows and macOS, measures in calibrated micrometres, keeps annotations attached to the slide, compares two slides side by side at matched scale, exports regions as GeoJSON for QuPath, and shares an exact field of view as a link. It runs on your own machine, does not need an image server, and is priced for a lab rather than a hospital. It is not a medical device and is not for primary diagnosis. If you are choosing between it and the free viewers, the whole slide image viewer comparison is the honest place to start.
Digital pathology glossary
- Whole slide image (WSI)
- A gigapixel, multi-resolution digital scan of an entire glass slide.
- Image pyramid
- The set of progressively downsampled, tiled copies of a whole slide image that lets a viewer show any zoom level quickly.
- MPP (microns per pixel)
- The physical size of one pixel at full resolution; the calibration every measurement depends on.
- 20x and 40x
- The objective magnification used during scanning, roughly 0.5 µm and 0.25 µm per pixel respectively.
- H&E
- Haematoxylin and eosin, the standard stain for tissue morphology.
- IHC
- Immunohistochemistry, a stain that marks a specific protein; often reviewed side by side with the H&E of the same block.
- Z-stack
- Several focal planes captured through a thick section so the viewer can refocus.
- DICOM WSI
- The DICOM standard's supplement for whole slide images, used to integrate pathology into hospital imaging systems.
- Image management system
- The server platform that stores, indexes, and serves whole slide images in a clinical laboratory.
- Computational pathology
- Image analysis and machine learning applied to whole slide images.
Questions people ask about digital pathology
What is the difference between digital pathology and computational pathology?
Digital pathology is the infrastructure: scanning slides, storing whole slide images, and viewing them on screen. Computational pathology is what you do with those images once they are digital: image analysis, cell counting, tissue classification, and machine learning models. You need the first before you can do the second.
Is digital pathology the same as telepathology?
No. Telepathology means reviewing pathology material remotely, which predates whole slide imaging and originally used live camera feeds from a microscope. Digital pathology makes telepathology far easier because a scanned slide can be shared as a file or a link, but a lab can be fully digital without ever consulting remotely.
What file format do digital pathology slides use?
There is no single format. Each scanner vendor writes its own: Aperio and Leica write SVS, Hamamatsu writes NDPI, 3DHISTECH writes MRXS, Leica SCN scanners write SCN, Ventana writes BIF, Philips writes iSyntax, and Olympus writes VSI. Vendor-neutral options are pyramidal TIFF, OME-TIFF, and DICOM whole slide imaging. A vendor-neutral viewer such as SlideScope reads most of these directly.
Do I need special hardware to view whole slide images?
No. Because a whole slide image is stored as a pyramid of tiles, a viewer only loads the tiles for the region and zoom level on screen. An ordinary laptop with 8 GB of RAM opens a multi-gigabyte slide in seconds. Scanning does need a slide scanner, and clinical primary diagnosis uses validated displays, but research and teaching review does not.
Can I do digital pathology on a Mac?
Yes, for viewing and research review. Several vendor viewers are Windows only, including Aperio ImageScope, but QuPath, ObjectiveView, Hamamatsu NDP.view2, and SlideScope all run on macOS. SlideScope ships native Apple Silicon and Intel builds and opens SVS, NDPI, MRXS, SCN, BIF, and QPTIFF slides on a Mac.
Open your first whole slide image
SlideScope's free trial includes every feature. Drop in an SVS, NDPI, or MRXS file and see the pyramid, the calibrated scale, and the annotation tools on your own slides.
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