Turn the microscope you already have into a whole-slide scanner.
Move the slide by hand and PixelScan WSI stitches every camera frame into one large, sharp slide.
View, measure and annotate it, then export Aperio SVS or OME-TIFF
that opens straight in QuPath. No motorised stage, no $50,000 scanner.
1,463tiles stitched into one 36,832 × 37,514 px slide
Exports open directly in
QuPath
OpenSlide
ASAP
HALO
Orbit
OMERO
Your microscope, now a slide scanner
Dedicated slide scanners cost $50,000–$200,000. You already have most of one.
A brightfield microscope, a camera and a Windows PC are all you need. Made for students, educators,
researchers and anyone who wants to digitise glass slides: H&E, special stains and IHC.
01
Connect a camera
Any USB microscope camera with a Windows driver works. No camera? Stitch a video of the slide or a folder of tiles instead.
02
Move the slide
Each frame is matched and added in the background. A marker shows where the camera is, and warns you if you move too far.
03
Export and analyse
Save a pyramidal SVS or OME-TIFF with the real pixel size, and open it in QuPath, OpenSlide, ASAP or OMERO.
Take the tour
From live view to a slide that opens in QuPath
Frames are added as you move the slide, and a box shows where the camera is.
Live demo
Zoom into a real slide scanned with PixelScan WSI
This H&E section was stitched from 1,463 microscope frames into one 36,832 × 37,514 pixel image.
Scroll or pinch to zoom, drag to move around.
Loading slide…
Overview
Shown for demonstration only. Tiles are compressed for the web; the original export is sharper.
Features
Everything from the first frame to the final pyramid
Stitching you can trust
Three ways to scan: a live camera, a video of the slide, or a folder of tiles (PNG, JPEG, TIFF, BMP)
Sub-pixel accuracy: feature matching, then refinement to a fraction of a pixel
Global alignment for tile folders, so errors don't build up across large grids
Seamless blending: multi-band blending hides seams and brightness steps
Even illumination: flat-field correction and exposure matching between tiles
Quality flags for weak matches and blurry frames, plus Undo (Ctrl+Z)
Real whole-slide files
Aperio SVS
Tiled pyramid with pixel size, magnification, label and macro images
OME-TIFF
OME-XML metadata for OMERO, QuPath and Fiji
Pyramidal TIFF · JPEG · PNG
For everything else
JPEG, JPEG 2000, WebP or lossless compression, with the file size estimated before you export.
A fast slide viewer
Opens SVS, NDPI, MRXS, SCN, BIF, OME-TIFF and more
Navigator, 1.25x–40x buttons and a live scale bar
Measure length, area, perimeter and angle
QuPath-compatible GeoJSON annotations
H&E / DAB separation and Macenko normalisation
Built for big slides
The mosaic is kept on disk, so gigapixel scans run on an ordinary PC
Autosave every 30 seconds, with crash recovery
Save projects and reopen them later
Progress bar, time left and Cancel for long jobs
True measurements
Calibrate each objective on a stage micrometer, or from the camera sensor
Pixel size is written into every export, so QuPath shows the right scale
Your images stay on your PC; nothing is uploaded
Supported cameras
11 camera driver families
Any USB camera with a standard Windows driver works. Dedicated microscope cameras use the maker's own software
when it's installed. Drivers marked Beta are new, so try your camera
during the free trial before you buy.
DirectShow / USB
Works
Webcams, USB microscope cameras, capture cards and virtual cameras
needs: nothing extra
TWAIN
Beta
Olympus / Evident DP series and other TWAIN sources
Not sure which one you need? If you use PixelScan WSI for an organisation or are paid for the work, you need the commercial licence.
Just ask.
FAQ
Common questions
Do I need a motorised stage?
No. Move the slide by hand. Each frame is placed as you go, and Auto-capture takes a new frame whenever the stitcher is ready.
Will my camera work?
Any USB camera with a standard Windows driver works. Drivers for Olympus/Evident, ToupTek/AmScope, Motic and scientific cameras are new, so try yours during the free trial. If it isn't listed, send a camera support request.
Will my slides open in QuPath?
Yes. SVS, OME-TIFF and pyramidal TIFF exports include the calibrated pixel size, and annotations are saved as GeoJSON that QuPath can import. They also open in OpenSlide, ASAP, HALO, Orbit and OMERO.
Are my slides uploaded anywhere?
No. Everything runs on your own PC, and PixelScan WSI doesn't upload your images.
What PC do I need?
Windows 10 or 11 (64-bit). For large scans, 8 GB of RAM or more and an SSD are recommended.
Can it be used for diagnosis?
No. PixelScan WSI is for education, research and personal use. It is not a medical device and must not be used for diagnosis or patient care.
Contact
Get in touch
Ask about a commercial or lab licence, request support for a camera, or ask anything else. Messages go straight to the developer.
