Image Processing and Guidance, PC1-PC5

Improve Your Imaging

Tips & tricks to get the best images

  

   

Find a suitable protocol

Learn More

Go Further

Extend your analyses

... with histology

For assistance and guidance on histology matters, contact Helene M. Andersen at the Histology Core Facility located at Biomedicine in the Skou building, 1116, room 270D.

... with Flow Cytometry

For studying host-pathogen interactions, use Imaging Flow Cytometry at the FACS Core Facility at Biomedicine.

Explore Our Gallery

Get inspired

... send us your favourite images that you are not planning on publishing anyway along with a few words for explanation and we will upload them here for others to enjoy.


Image Processing PCs

   
  • Registered users may perform advanced image processing using personal computers or our dedicated Image Processing PCs (PC1-PC5). Please contact The Bioimaging Team to get started.
  • All image processing PCs can be accessed remotely either on the AU network or from home via vpn.
   

Need help?

Come to our Open Office sessions to discuss your imaging needs or get advice on workflows, free of charge:

Tuesdays and Thursdays

13:30 -14:30

The Skou building, 1116-256

   

Or contact us on:


PC1

3D and 4D image processing and deconvolution

Location: building 1116, room 270E 

   

  *) This PC has a Nvidia RTX 2070 graphics card for high performance image processing.  

What is deconvolution?

Deconvolution makes your images nice and crisp. This image processing technique improves contrast and resolution of images captured by light microscopy. Out of focus light causes blur which mathematically is represented as a convolution operation. Deconvolution seeks to reassign out of focus light to the correct origin. Nearly all fluorescence images can be deconvolved.

PC2

Zen, cellSens and DIC image acqusition

Location: building 1116, room 368

   

  *) This PC has an ASUS DUAL-GTX1660S-6G-EVO graphics card for high performance image processing.


Bright-field DIC microscope

For rutine check of stained and unstained cells or tissue.

   

Semi-motorized bright-field inverted microscope (no fluorescence) with a sensitive color camera and heating stage, controlled by Image processing PC2.

Objectives

Please note: all objectives are dry objectives

5x, 10x (Ph), 20x (Ph), 40x (Ph)

40x (DIC), 63x (DIC)

Contrast methods

Phase contrast (Ph) and Differential Interference Contrast (DIC)


PC3

Kuant for Newton 7.0 and IVIS software

   

Location: building 1116, room 368

   
  • Processing of data from the Newton 7.0 in vivo imaging system
    • Kuant freeware is currently only available for Windows
  • Advanced processing of data from the In vivo imaging system (IVIS)


PC4

Selection of image processing software

   

Location: building 1116, 368

   
  • Scan^R for high content imaging data analysis 
  • Zen lite
  • Fiji
  • Ilastik 
  • Olympus Xcellence

   

   


PC5

Arivis vision 4D

Location: building 1116, room 550

   

  • Arivis Vision 4D for 2D, 3D and 4D visualization, annotation, and image batch processing regardless of image size
  • MATLAB
  • Freeware like Fiji and Ilastik 

This PC has a Nvidia RTX 2070 super graphics card for high performance image processing.  


Software Packages and Freeware

Fiji/ImageJ

Fiji is ImageJ with additional plugins e.g. allowing opening of multiple file formats.

How do I download Fiji/ImageJ?

Fiji can be downleade here.

   

1. Download the correct version for your system (Win64/32, Mac, Linux64/32) 

2. Place the file on your desktop or somewhere else that you administrate ("program files" folder is not recommended)

3. Run the ".exe file" (eg. ImageJ-win64)

4. Accept Update of ImageJ upon first start up

How do I open Olympus (.vsi) files in Fiji?

Go to: https://imagej.nih.gov/ij/docs/guide/146.html

In order to open Olympus (.vsi) files, please follow this guide:

  • download Bioformat plugin
  • open Fiji folder in file explorer, e.g.: C:\Users\xxxxxx\Documents\Fiji\Fiji.app\plugins
  • replace the "Bioformat plugin x.x" with the one you have downloaded and unzipped
  • open Fiji - Plugin - Bio-format importer and select your file(s) 

QuPath

QuPath is a powerful user-friendly bioimage analysis software designed to extract quantitative information from microscopy images. QuPath is optimised to process whole slide images from digital pathology, but it can also handle 2D images acquired by most fluorescence microscopes.

Common uses include identification, measurement and classification of nuclei, cells and regions of interest in the images. 

Cell Profiler/Cell Analyst

Cell Profiler/Cell Analyst – Image Batch Processing and Data Analysis

The scikit-image SciKit (toolkit for SciPy)

The scikit-image SciKit - (toolkit for SciPy) extends scipy.ndimage to provide a versatile set of image processing routines. It is written in the Python language.   

ICY

ICY - An open community platform for bioimage informatics

MATLAB

What is MATLAB?

Our sensitive high-resolution microscopes generate large volumes of data that may contain insights linking structure and function at the molecular, cellular, or tissue level, and may be used to decipher mechanisms and energetics of biological processes. The powerful programming software MATLAB may e.g. be used for:

   

MATLAB is installed on our Image Processing PC1 and PC2 running smoothly thanks to the powerful GPUs of our PCs.

Ilastik

Leverage machine learning algorithms to easily segment, classify, track and count your cells or other experimental data. Most operations are interactive, even on large datasets. You only need to draw the labels and will immediately see the result.   

No machine learning expertise is required.

Insight toolkit (ITK)

Insight toolkit (ITK) -  an open-source, cross-platform library that provides developers with an extensive suite of software tools for image analysis

The Visualization Toolkit (VTK)

The Visualization Toolkit (VTK) - an open-source software system for 3D computer graphics, modeling, image processing, volume rendering, scientific visualization, and 2D plotting

OpenCV

OpenCV - an open source computer vision and machine learning software library.