Biomedical Imaging Research Unit

MetaSystems VSlide slide scanner

BIRU webinar - Super-Multiplexed Imaging


  • Whole section scanning
  • Region of interest scanning including setting up a scan field (region of interest) at low magnification and then scanning the ROI at higher magnifcation/resolution.
  • Tissue microarray scanning and on the fly analysis
  • Brightfield, high resolution brightfield (using the monochrome camera) or fluorescence


CoolCube1 (colour) CCD

CoolCube 4m TEC (monochrome) sCMOS
Camera upgrade funded by the Liggins Institute in 2019

  • resolution 4096 x 300 pixels (12MPixel)
  • 30 frames per second read-out speed
  • pixel size 3.45 x 3.45 microns
  • thermo-electric cooling


Fluorescence light source

Solid-State Light Source Colibri 7

7 solid state LED lamps - wavelengths below

UV (385nm) for excitation of DAPI, Alexa 405, Hoechst 33258 and similar dyes

Violet (430nm) for excitation of eCFP, Lucifer Yellow, Alexa 430 and similar dyes

Blue (475nm) for excitation of eGFP, Fluo4, FITC and similar dyes

Green (555nm) for excitation of Cy3, TRITC, DsRed and similar dyes

Yellow (590nm) for excitation of mCherry, Alexa 568, mPlum and similar dyes

Red (630nm) for excitation of Cy5, Alexa 631, TOTO-3 and similar dyes

Far Red (735nm) for excitation of Cy7 and similar dyes

Band width details  available here


Microscope specifications/software

  • Zeiss Axio Imager Z2 fully motorised microscope
  • Egonomic driver for XY control
  • Automated 80 slide feeder
  • Objectives: Dry (2.5x/0.075 NA, 10x/0.45 NA, 20x/0.9 NA, 40x/0.95 NA) Oil (40x/1.3 NA, 63x/1.4 NA)
  • Automated oiler module
  • Marzhauser Motorised 5 position scanning stage
  • MetaCyte acquisition software and stitching
  • On the fly TMA (tissue microarray) analysis

Fluorescence filter sets

Multiband filter sets

81 HE – QUAD filter, suitable for fluorescent dye combinations  like DAPI, FITC, DsRed, Cy5
Uses LEDs 385, 475, 555, 630nm
Collects emission bands 375/38 + 484/25 + 553/18 + 631/22
Spectra here

112HE – PENTA filter, suitable for fluorescent dye combinations  like DAPI, FITC, DsRed, Cy5 and Cy7
Uses LEDs 385, 475, 555, 630, 735nm
Collects emission bands 425/30 + 514/31 + 592/25 + 681/45 + 785/38
Spectra here

Single band filter sets

Filter set #01  (Use LED 385; Em- 447/60nm) - spectra

Filter set #02  (Use LED 430; Em-550/32nm) - spectra

Filter set #03  (Use LED 475; Em 527/20nm) - spectra

Filter set #04  (Use LED 555nm; Em 580/23nm) - spectra

Filter set #05   (Use LED 590; Em 628/32) - spectra

Filter set #06    (Use LED 630; Em 676/29nm) - spectra

Filter set #07     (Use LED 735; Em 809/81nm)  - spectra


If you want to see some additional examples which illustrate what can be done with this system, please take a look at the movies below which were created by Luke Hammond from QBI Microscopy using his VSlide.

Support files

ImageJ macros for cropping borders from extracted images:

(1.0 kB, TEXT)
(994.0 bytes, TEXT)
Using the ImageJ macros
(276.6 kB, PDF)

IrfanView - Instructions for cropping extracted images
This document explains how to use open source software IrfanView to crop off the white/black boxes from extracted images. (740.1 kB, PDF)

Funded by

Successful grant application by Professor Mike Dragunow (Dept of Pharmacology & Centre for Brain Research) to Gravida: National Centre for Growth and Development

The system was upgraded with a CoolCube 4mTEC monochrome sCMOS camera funded by the Liggins Institute in 2019


Room extension number



Equipment charges - users from The University of Auckland

Subscription rate: $50.00 per hour (10 hours minimum) – pay in advance

Casual rate: $59.36 per hour – pay as you go

Contact people

Ratish Kurian

IT Systems Specialist - BIRU
Phone: +64 (0) 9 923 6195


Dr Richard Yulo

Senior Technologist
Phone: +64 (0) 9 373 7831