Zeiss Axioscan

Slide Scanner · Zeiss

A fully automated high-throughput slide scanning system. With a 100-slide capacity, 7-LED illumination, and 10×/20×/40× objectives, it is ideal for large cohort tissue section studies in both brightfield and fluorescence.

Instrument Features

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100-Slide Automated Magazine

Motorized slide loader holds up to 100 standard slides. Fully automated loading, scanning, and unloading allows unattended overnight batch runs — ideal for large cohort studies, clinical samples, or high-throughput screening.

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7-LED Illumination

7 independently controlled LED channels cover UV through far-red wavelengths. LED illumination provides instant on/off switching, consistent intensity, and long operational lifetime. Excitation – 385nm, 430nm, 475nm, 555nm, 630nm & 735nm and transmitted light channels.

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10× / 20× / 40× Objectives

Three objective magnifications for flexible resolution and throughput trade-offs. 10× for overview tissue architecture and large-area mapping, 20× for cellular resolution across whole sections, 40× for subcellular detail in targeted regions.

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Brightfield & Fluorescence

Supports H&E, IHC (brightfield), and multi-channel fluorescence scanning in a single run. Transmitted light mode for standard histological stains; reflected light for fluorescent tissue sections, IF-stained slides, and FISH.

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Automated Focus & Tissue Detection

Hardware autofocus and automated tissue detection algorithms locate and scan only the tissue area on each slide, reducing scan time and file sizes. Z-stack scanning available for thick sections or 3D tissue analysis.

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ZEN Slidescan Software

Centralized batch management, scan profile creation, and image stitching. Outputs standard CZI or OME-TIFF files compatible with ImageJ, QuPath, HALO, and other image analysis platforms for downstream quantification.

Startup Guide

1

Zeiss Axioscan: Startup and Slide Scanning Guide

The Axioscan is always on, so there is nothing to switch on.

  1. Log in to the computer using the login instructions on the desk.
  2. Detailed imaging instructions can be found on the computer desktop. Numbers in this guide refer to numbers on the desktop instructions
2

Before you start

The Zeiss AxioScan.Z1 slide scanner at the Optical Biology Core scans up to 100 slides in one run, supports unattended overnight imaging, and uses automatic tissue detection to draw several regions of interest per slide. It images brightfield (colour) and fluorescence slides. It has a Colibri 7 LED light source and is always on. Book time in iLabs and complete training before scanning alone.

ObjectiveNumerical aperture
5x Fluar0.25
10x Plan-Apochromat0.45
20x Plan-Apochromat0.80
40x Plan-Apochromat Korr0.95
3

Load your slides

  1. Click Open to open the slide scanner door.
  2. Remove a slide tray and place it on the slide holder. The holder opens the tray frame so slides are easy to insert.
  3. Place your slides face up with the label between the holder. Press the silver button to open the device [3].
  4. Make sure the slides are securely inside the trays.
  5. Put the trays back inside and click Close to shut the door.
4

Log in and start ZEN

The Axioscan is always on, so there is nothing to switch on.
Log in to the Axioscan computer using the login instructions on the desk.
Open ZEN Blue. The microscope initialises and takes an overview scan of the loaded slides, by tray and position
Open the Magazine tab to see all trays and slides
Under Storage Location, create a folder on the DATA (D:) drive for your lab and then one for yourself, and make sure that folder is selected

5

Set up your scan

  1. Load settings. Load either the global settings for all your slides, or the settings for individual slides
  2. Adapt the profile. Expand the star icon (1) to adapt the selected profile to your slide, then click Next through the setup steps (3).
  3. Tissue detection settings (4). These control how tissue is found on the slide. The default is manual. Fluorescently labelled tissue is sometimes hard to detect automatically, so fine tune the specimen histogram range in the sample detection tab until recognition is as accurate as possible. In some cases you must delete or add regions of interest by hand. Click Next.
  4. Coarse sample detection (5x objective). Go to Live (5), use AF (autofocus), and scroll to the bottom to see the focus point distribution options. A good choice is Every Nth row and column (6). Move the focus points so they sit inside the tissue, and avoid bubbles and debris Click Next.
  5. Fine focus map. Use the same objective you will image with, and repeat the same steps to adjust the focus points [3]. Click Next.
  6. Scan settings. Set these for your slide type:
    • Brightfield: adjust the white balance. Move to a blank area of the slide, expand Acquisition Mode and click Auto (7).
    • Fluorescence: adjust LED power and exposure time for each channel so the histogram fills at least 25%.
  7. Click Finish when all settings are done.
6

Scan and finish

  1. Click Start Scan. The predicted time is never right, so do not rely on it [3].
  2. After the first slide finishes, change your iLabs booking to the time it will really take to image all your slides [3].
  3. Overnight runs of 50 to 100 slides must be pre approved by Adeela, and the output drive must be cleared first [2].
  4. When the scan is done, click Open, remove your trays and slides, and click Close.
  5. Copy your data off the computer. Do not leave it on the instrument drive.
7

Start Batch Processing

See Adeela for more information

8

Review & Export

After scanning, review images in ZEN Slidescan viewer. Export to TIFF, OME-TIFF, or BigTIFF for use in QuPath, HALO, or ImageJ. Archive raw CZI files to your lab storage before clearing the instrument data drive.

9

Shut Down

Remove slide magazine and retrieve your slides. Exit out of ZEN. Computer and microscope stay ON.

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