Axio Scan.Z1

2 Agenda 1. Why do we need to Whole slide scanning? 2. What can you do with a virtual slide? 3. Axioscan. Z1 system

3 Axioscan. Z1 Why do we need to Whole slide scanning? Retain valuable information - Electronic journals - Credibility of images and data - Specimen quality Microscopes used efficiently - Advanced 3D microscopes used for routine 2D imaging - Diversity of applications Great images with data analysis - High-content image analysis solutions - Open source communities are driving applications - The need to share is information greater than ever

4 Axio Scan. Z1 Whole Slide Imaging -Archive and manage experimental image data -Routine imagine efficient -Fast & easy image analysis

5 Axioscan. Z1 What can you do with a virtual slide? Scanning a microscope slide with Axio Scan.Z1 will lead to five main outcomes for the researcher, clinician, or educator. What does Carl Zeiss do to support these outcomes?

6 Axioscan. Z1 Archiving and Management ZEN Browser is the database for Axio Scan.Z1 Administrators can control access rights to slides Start with 22Tb for 22,000 slides at 1Gb/slide ZEN Browser also runs on your existing compatible server hardware

7 Axioscan. Z1 Sharing and remote viewing Use the ZEN Browser app available free for Apple iPad View slides with ZEN Browser interface for the web: PC, Mac or Tablet Open virtual slides in your existing ZEN program Export images in a wide variety of popular formats The CZI file format is flexible and open

8 Axioscan. Z1 Consultation and meta data Annotate slides using any of the ZEN viewing platforms Freely store and access virtual slide meta data Compare slides side-by-side in ZEN Gallery View Collaboration is global – take your slides with you

9 Axioscan. Z1 E-learning Bring the latest research into the lecture room Communicate results and progress more effectively Remove distance as a barrier to learning Carl Zeiss works with specialist e-learning partners

10 Axioscan. Z1 Image Analysis: ZEN and beyond ZEN Image Analysis and ZEN Open Application Development Open and process CZI format in third-party software You chose the best solution for your investigation

11 Batch capacity of up to 100 slides (1” x 3”), 12 slides version is also available Barcode reading Handling of 1”x3” and 2"x3" slides (trays) Modular design (Entry-Level device can upgraded to High-End device) Slide and tray detection already inside magazine up to two cameras to get best results for BF and FL BF and FL / Ring aperture contrast in one device Colibri.2 and/or HXP 120 V ZEN lite can be used to view images (free viewer) Technical Details System Overview

12 Technical Details 1 Objectives Fluar 5x (New)

13 3 chip camera (color) 2 MP 30 fps / 12 bit / 4.4 µm*pixel-1 1 chip camera (b/w) 1.4 MP / 11 frame / 12bit / 6.5 µm*pixel -1 1 chip camera (b/w) 4 MP frame / 16bit / 6.5 µm*pixel -1 1 The effective region of interest, which will be used for scanning, can be smaller 2 The effective frame rate could be lower Technical Details 2 Cameras

14 Axio Scan.Z1 holds a maximum of 100 slides at any time Four standard slides are held in a single framer Large format slides (50mm x 75mm) can be used Slides can be loaded and unloaded during scanning Key advantage: Carl Zeiss uses a very reliable loading mechanism Technical Details 3 Slide loading

15 Technical Details 4 Illumination & Filter wheel Synchronous 50ms channel switching for 5 colours Colibri 2 high performance LED illumination HXP 120V metal halide (extended option) Full ZEN fluorescence functionality including smart set-up Captures fluorescence faster and in superior quality

16 Focus map created at low and high magnification for accuracy Number of points is variable and relates to sample flatness Different spatial distribution algorithms available Focus fluorescence by selected channel or brightfield image Key advantage: Focusing of specimen is accurate and reproducible with Axio Scan.Z1 16 Technical Details 5 Focus strategy

17 Three main methods for tissue detection: 1.Automatic threshold 2.Manual identification 3.Ring aperture contrast for unstained tissue (fluorescence) Each method can be adapted and specialised Key advantage: A wide range of specimen types can be automatically detected including fluorescence Technical Details 6 Tissue detection

18 Focusing and stitching is done while scanning Scan speed is approximately 2cm 2 per minute at 20x Z-stack images can be acquired during scanning Key advantage: Axio Scan.Z1 is fast but does not compromise superior image resolution Technical Details 7 Scanning

19 Axio Scan.Z1 generates pyramidal image files Annotations are stored in a separate image layer CZI files can be converted to TIFF, JPEG, and TIFF Key advantage: Axio Scan.Z1 images are fast to view and flexible for analysis 19 Technical Details 8 CZI File format

20 Neurobiology Application Amyloid Plaques Quantification Example from a customer sample. This example is done with ZEN blue (Image analysis module)

21 Axio Scan. Z1 -System Overview

22 22 ZEISS in Focus