Slide Scanner Service

The Imaging & Optics Facility provides a full Image Acquisition Service for Slide-Scanning. One main advantages for using this service is that the acquisition is performed by Imaging and optics Facility staff – which can save time for your other research tasks. The service offers:

  • Option to choose and combine different imaging modality (brightfield or fluorescence)
  • Generation of overview scans for fast screening and sample navigation (see point 6)
  • 2D or 3D imaging capabilities.
  • Include high-resolution imaging of selected Regions Of Interest (ROIs), including shading correction & stitching
  • Optional: scene splitting, further post processing and image analysis routine: deconvolution, segmentation
  • Scanned images can be used for navigation on LSM confocal microscopes via ZEN Connect

The Slide Scanner Service makes use of the Zeiss Axioscan Z1. All specification in the form of available imaging modalities (brightfield, color and fluorescent), fluorecent excitation and objectives can be found at the system specification

We are happy to explore options to elaborate this service with projects to set up “whole-analysis pipelines”, that include: i) Acquisition → ii) Image Processing (stitching, deconvolution) → iii) Image Analysis (segmentation & object counting / classification)

Service Information

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

A first ‘Slide Scanning Request’ 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 all fields – as this speeds up the process

3. After submitting the Slide-Scanner Service Request form,you will be approach by IOF staff to discuss the project and to set up an ‘Acquisition profile’ for the project with a representative slide of yours

  • 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)

4. You will receive an Excel list containing the names used for the slides, and a column to add the slide name, to later on identify the slides from the file names 

5. You will further receive QR codes to be attached on the frosting of your slide; the machine automatically reads out the encoded slide name, saving time during the setup of the imaging assisted by IOF staff

6. 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

Request: Slide-Scanner Acquisition Service

Zen Connect

Zen Connect → Navigating and Generating Image Overlays
Zen Connect allows to reopen overview slide scanner overview scans and add additional lasyer of data (e.g. LSM confocals data). This allows to allowing to easily navigate on the slidescanner-data to set Regions Of Interest (ROIs) to add additional layers of confocal data, in case required. This the generated multi-dimensional dataset (widefield + Confocal / airyscan- data) that can be opened with the free version ZEN Lite, or imported in Bitplane Imaris for further analysis.

Request: Assited session for a ZEN connect

Zen Connect → Available Instrumentation
Zen Connect projects can be made offline within the free ZEN Lite v3.4. project data from the Axioscan Slidescanner can be used for navigation and aquisition on the following confocal micrscopes: LSM800-01, LSM800-02, LSM800-03, LSM800-04

Request: Assited session for a ZEN connect