Axio Scan

NEW: ZEISS Axio Scan.Z1 Slide Scanner

Digitise your samples on slides using the fast, reliable ZEISS AxioScan Z.1 microscope! This slide-scanning microscope has both bright-field and fluorescence imaging capabilities and can create virtual images of whole slides or defined regions of interest. The system can hold up to 100 slides at one time and therefore allows high throughput slide-scanning. For more information or to book in for training, please contact Sadaf Kalam, Facility Manager, Bosch Institute Advanced Microscopy Facility ().

Axioscan image

Axio Scan.Z1 Slide Scanner with 100 slide capacity. Objectives 2.5x, 10x, 20x and 40x high NA with RAC contrast for imaging of unstained specimens. High speed excitation, emission and dichroic filter wheels for high speed fluorescent image capture via 4 MPixel sCMOS camera. Filtersets for DAPI, FITC, Cy3 and Cy5. System also has 2 MPixel 3 CCD colour camera for high speed brightfield imaging.

User Feedback:

“It is absolutely WONDERFUL! What took me 1 month to do last time, only took me 8 hours on the Axioscan! Now I am able to present new data at a conference next week. Thank you!!!!!” Bianca McCarthy, Physiology, The University of Sydney

Funding for this microscope was kindly provided by The University of Sydney DVC Research/Equipment Grant 2013, School of Medical Sciences, Bosch Institute, Pathology and RIBG 2013.

Data management information for AxioScan users

The AxioScan.Z1 can quickly generate many gigabytes of data. We advise AxioScan users to utilise digital storage space on the Sydney RDS for their AxioScan files. Go to the Sydney Research Data Management Planning Tool to create your data management plan and request up to 2 TB digital storage space on the RDS.

FL image
BF test image
AxioScan detailed specifications:

The Axio Scan.Z1 system at the Bosch AMF consists of the following main components:

  • Z-drive with 3mm usable focus range
  • Magazine for 100 slides 26x76mm
  • Support for mounting 1 x 2 slides 52x76mm
  • Filter set 49 DAPI shift free
  • Filter set 44 FITC BP special, d=25 shift free
  • Filter set 50 Cy 5 shift free
  • Filter set 43 Cy 3 d=25 shift free (E)
  • Objective Fluar 2.5x/0.12 M27
  • Objective Plan-Apochromat 10x/0.45 M27
  • Objective Plan-Apochromat 20x/0.8 M27
  • Objective Plan-Apochromat 40x/0.95 Corr M27
  • Camera Set 3CCD Hitachi HV-F202SCL for Axio Scan.Z1
  • Camera Set Orca Flash 4.0 for Axio Scan.Z1

Slide Scanning Service

The AMF is pleased to offer a slide scanning service on the AxioScan.Z1. We can scan your brightfield or fluorescent slides for you. Scan files (.czi format) can be viewed in ZEN lite software (available free for download from the ZEISS website).

Download the sample submission form to view the terms of service. A sample submission form should be completed for all slide sets to be scanned.

For more information or to book in for the slide scanning service, please contact Sadaf Kalam, ().

Slide-scanning charges

School of Medical Sciences

University of Sydney


Brightfield imaging, per slide




Fluorescent imaging, per slide
(up to 4 channels)




Set up fee – paid once per type of slide (e.g. for different antibodies, FL channel combination etc)