Slide Scanner Service – Imaging & Optics Facility

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

Slide-Scanner Specification

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 Request 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

QR-Codes are provided 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

Ideal for larger batches: Histology or Fluorescent, samples.

QR codes are provided as labels

Multiple serial Sections can be placed on one slide

The sections are detected, or custom Regions Of Interest (ROI) can be defined to acquired multi-tile stack images

Z-projection of an 3-channel multi-tiled image stack

Additional Image Analysis requirements?

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)

Please explore our Image Analysis Services, to explore our image analysis infrastrucrure, or ask to request image analysis support.

Service Information

Additional Image Analysis requirements?

Zen Connect