Whole-slide imaging for Windows

Turn the microscope you already have into a whole-slide scanner.

PixelScan WSI stitches live camera frames, videos or tile folders into one large slide image, then exports Aperio SVS, OME-TIFF and pyramidal TIFF that open directly in QuPath and OpenSlide. There's no $50k scanner to buy.

Get it from Microsoft
14-day free trial Then a one-time purchase
Need it for a lab, hospital or company? Get a commercial licence →
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 PixelScan WSI needs. Move the stage by hand and the slide builds up on screen as you go.

  1. 01

    Connect your camera

    Any USB microscope camera with a Windows driver works. There are also drivers for ToupTek/AmScope, Motic, Olympus/Evident and scientific cameras.

  2. 02

    Move the stage

    Frames are stitched live on their own thread, and auto-capture grabs a frame whenever the stitcher is ready. Made a wrong move? Undo it.

  3. 03

    Export and analyse

    Save a pyramidal SVS or OME-TIFF with the real pixel size and open it in QuPath, OpenSlide, ASAP, HALO, Orbit or OMERO.

Dedicated WSI scanner

$50k–$200k

  • New hardware, service contract, bench space
  • Often one shared scanner per department

PixelScan WSI

One-time purchase

  • Uses the microscope and camera you already own
  • Try it free for 14 days first

See it in action

From live view to a slide that opens in QuPath

Demo video placeholder

media/demo.mp4 · 20–30 s

PixelScan WSI stitching live camera frames into a slide

Screenshot placeholder

01-live-stitching.png

Live stitching
A whole-slide image open in the PixelScan WSI viewer

Screenshot placeholder

02-viewer.png

Slide viewer
The export dialog with SVS, OME-TIFF and TIFF options

Screenshot placeholder

03-export.png

Export dialog
Measurements and annotations on a tissue slide

Screenshot placeholder

04-measurements.png

Measurements & annotations
The camera list showing detected camera drivers

Screenshot placeholder

05-cameras.png

Camera selection

Features

Everything from the first frame to the final pyramid

Stitching that holds up

  • Three sources: a live camera, a video file, or a folder of tiles (PNG, JPEG, TIFF, BMP)
  • Accurate placement: ORB feature matching with sub-pixel refinement, plus global alignment that solves every tile position together
  • Fast, Balanced or Best quality. Best uses multi-band blending for invisible seams
  • Clean images: flat-field correction, exposure matching between tiles, and quality flags for blurry frames or weak matches

Export for real pathology tools

Aperio SVS
Tiled pyramid with pixel size, magnification, label and macro images
OME-TIFF
Sub-IFD pyramid with OME-XML metadata
Pyramidal TIFF
Tiled BigTIFF with resolution tags
JPEG / PNG
A single flat image

Compression options: JPEG, JPEG 2000, WebP, LZW, Deflate or none. You can export the whole grid, only the scanned area, or tissue only.

A viewer for any slide

  • Opens SVS, NDPI, MRXS, SCN, BIF, OME-TIFF and more
  • Navigator, 1.25x–40x magnification and a scale bar
  • Measure length, area and angle in µm and mm²
  • Annotations saved as QuPath-compatible GeoJSON
  • H&E / DAB colour deconvolution and Macenko normalisation

Any slide size, safely

  • Tiles are kept on disk with a fixed RAM budget, so slide size is limited by disk space, not memory
  • Exports are written piece by piece
  • Autosave every 30 seconds, with crash recovery
  • Save and reopen projects as .scan files

Calibrated to real microns

  • µm per pixel for each objective
  • Measure it on a stage micrometer, type it in, or compute it from the camera sensor and adapter
  • Written into every exported slide, so QuPath gets the right scale

Supported cameras

11 camera driver families

Any USB camera with a Windows driver works through DirectShow. Vendor drivers load the camera maker's own software, so if it's installed, the camera shows up. Vendor drivers marked Beta are implemented but still being tested on real hardware.

DirectShow / USB

Works

Webcams, USB microscope cameras with a Windows driver, virtual cameras

needs: nothing extra

TWAIN

Beta

Olympus / Evident DP series and other TWAIN sources

needs: vendor TWAIN driver

ToupTek family

Beta

ToupTek, AmScope, OMAX, Euromex, Altair, MallinCam, SVBONY and rebrands

needs: camera software (DLL)

Motic

Beta

Moticam S / Pro S, MC, MA and Swift MC series

needs: Motic Images Plus

Basler

Beta

ace, ace 2, dart, boost

needs: pylon

Teledyne FLIR

Beta

Blackfly S, Grasshopper3, Chameleon3, Oryx

needs: Spinnaker

IDS

Beta

uEye USB / GigE

needs: IDS Software Suite

Allied Vision

Beta

Alvium, Mako, Manta, Prosilica

needs: Vimba X

Hamamatsu

Beta

ORCA series

needs: DCAM-API

Teledyne Photometrics

Beta

Prime, Kinetix, Iris, Retiga

needs: PVCAM

Andor

Beta

Zyla, Sona, Neo, Marana (sCMOS)

needs: Andor SDK3

Camera not listed?

Tell me the make and model and I'll look at adding it.

Request camera support →

Pricing

Two simple licences

Personal

Microsoft Store

One-time purchase · 14-day free trial

  • Every scanning, viewing and export feature
  • Installs and updates through the Microsoft Store
  • For your own learning, study, hobby or private research
  • Personal, non-commercial use only
Get it from Microsoft

Commercial / Lab

Contact me

Terms arranged for your organisation

  • Hospitals, laboratories, universities and companies
  • Any use by or for an organisation, or paid work
  • Integration, bundling and automation with other software
  • Direct contact with the developer
Request a commercial licence

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 stage by hand. PixelScan WSI stitches each frame as you go, and auto-capture takes a new frame whenever the stitcher is ready.

Will my camera work?

Any USB camera with a Windows driver works through DirectShow. Drivers for ToupTek/AmScope, Motic, Olympus/Evident (TWAIN) and scientific cameras are in beta. If yours 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 QuPath-compatible GeoJSON. They also open in OpenSlide, ASAP, HALO, Orbit and OMERO.

How large can a scan be?

The mosaic is stored in tiles on disk with a fixed memory budget, and exports are written piece by piece. Slide size is limited by free disk space, not by RAM.

Which systems does it run on?

Windows 10 and Windows 11, installed from the Microsoft Store.

Can it be used for diagnosis?

No. PixelScan WSI is for research use only and is not a medical device. Do not use it for diagnosis.

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.

Or email contact@pixelscanwsi.com