Zeiss AxioScan Z1 Slide Scanner

Location:  room I06.U1.405 / LBE

The Imaging & Optics Facility provides a full slide-scanner service → details Slide Scanner Service

ZEISS Axio Scan.Z1 Slide Scanner


  • 25 mounting frames for 4 slides (= 100 slides loading capacity in 1 time)
  • Bright field imaging
  • Fluorescent
Contrast techniques:
  • TL Brightfield
  • TL Ring Aperature Contrast (RAC)

Light sourse: 7 solid state LED lamps (Kolibri 7)
  • Red (630nm) for excitation of Cy5, Alexa 631, TOTO-3 and similar dyes
  • Yellow (590nm) for excitation of mCherry, Alexa 568, mPlum and similar dyes
  • Green (555nm) for excitation of Cy3, TRITC, DsRed and similar dyes
  • Cyan (511nm) for excitation of eYFP, Eosin, TOTO-1 and similar dyes
  • Blue (475nm) for excitation of eGFP, Fluo4, FITC and similar dyes
  • Violet (430nm) for excitation of eCFP, Lucifer Yellow, Alexa 430 and similar dyes
  • UV (385nm) for excitation of DAPI, Alexa 405, Hoechst 33258 and similar dyes

  • Fluar 5x/0.25 M27 (FWD=12.5mm)
  • Plan-Apochromat 10x/0.45 M27 (FWD=2.1mm)
  • Plan-Apochromat 20x/0.8 M27
  • Plan-Apochromat 40x/0.95 Corr M27 (FWD=0.25mm)

  • Color camera: Hitachi HV F202  (Histology)
  • Monochrome: Hamamatsu Orca Flash 4.0 V3 (Fluorescence)


  • ZEN Connect
  • ZEN Module Macro Environment
  • ZEN Module Image Analysis
  • ZEN Module Advanced Processing & Analysis
  • ZEN Module Intellesis

Information: How to make use of the Slides Scanner Service?
How to get your slides scanned?

  • More detailed description of the available Slides Scanner service can be found on the Slides Scanner Service page → details Slide Scanner Service
  • A first ‘Slide Scanning Request’, we will require an ‘assisted session’ to establish the ‘acquisition protocol’. This also accounts for any request with samples that significantly differ from previous established protocols!

1. Select the Request-tab in PPMS;

2. Select and fill out the Slide Scanner Service Reqest Form , and fill out al fields – as this speeds up the process;

3. After submitting the Slidescanner Service Request form,you will be approach by IOF staff to discuss the project and to set up an ‘Acquisition profile’ for the project;

4. For the setup of the ‘Acquisition profile’  we will invite you to bring your slides to our office in i06.EG.108

  • It is possible to mark the sections with a marker pen to facilitate and speed up tissue detection
  • Various Bar- and QR-Codes are supported for slide naming (see product info sheet)

5. After completion, you will get notified that your data has been copied to your scratch-folder and that your sampled can be collected again from our office in i06.EG.108