Image Processing

Remote desktop

Image processing PC1, PC2, PC3, PC4 and PC5 can now be accessed remotely (on the au network / from home via vpn)

Image Processing PC1: 3D and 4D Image processing and deconvolution

With PC1 in room 270E you can process your images using: 

  • Imaris 8.2 single full for 3D/4D visualization and image processing *)  
    • NOTE: Imaris does not work via Remote Desktop
  • cellSens dimention v2.3 with "count and measure" and "Constraied iterative deconvolution" **)
  • Scan^R for high content imaging data analysis 
  • Freeware like Fiji and Ilastik 

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

Learn about deconvolution

Deconvolution is an image processing technique used to improve contrast and resolution of images. Out of focus light causes blur which mathetically is represented as a convolution operation. Deconvolution seeks to reassign out of focus light to the correct origion. Nearly all fluorescence images can be deconvolved.

Introduction to PC1 - Video

Imaging PC1
Book Imaging PC1

Image processing PC2: Zen, cellSens and DIC image acqusition

With Image Processing PC2 in room 368 you can do:

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

Book Imaging PC2 and Inverted DIC microscope

Image processing PC3 (IVIS)

With Image Processing PC3 in room 368 you can do:

  • Advanced processing of data from the In vivo imaging system (IVIS)


Book Imaging PC3 (IVIS)

Image processing PC4

With PC4 in room 368 you can process your images using: 

  • Scan^R for high content imaging data analysis 
  • Zen lite
  • Fiji
  • Ilastik 
  • Olympus Xcellence
Book Imaging PC4 (Scan^R and Xcellence)

Collection of our software and available freeware

Here is a collection of our software and available freeware. Users can perform advanced Image Processing using personal computers or our dedicated Imaging Processing PCs. Please contact The Bioimaging Team to get started.

Software packages of interest for some facility users


Learn more about MATLAB

Our sensitive, fast and high-resolution microscopes generate large volumes of data, and as a result you have the posibility to do powerful and complex processing of your data. Data may contain insights linking structure and function at the molecular, cellular, or tissue level, and it can be used to decipher mechanisms and energetics of biological processes. In order to do so you need powerful programming software. Below you can find inspiration copied from the MATLAB website   

MATLAB is installed on our Imaging PC1 or PC2 (see above) and can take advantage of the powerful GPUs of our PCs.

As an AU employee you can also install MATLAB (see button below) on you own PC (dont forget to log on VPN)

Freeware of interest for some facility users


*Don´t be confused! Fiji is just imageJ but with useful plugins (eg. plugins to open multiple file formats)

How to download Fiji/ImageJ

Please download Fiji 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 (maybe not "program files" folder)

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

4. Accept Update of imageJ* upon first start up

How to open Olympus (.vsi) files in Fiji


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

Download Bioformat plugin from here:

open fiji folder in file explorer, eg: 


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) 

Free Interactive Machine Learning for image analysis

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 just draw the labels and immediately see the result. No machine learning expertise required.

Cell Profiler/Celle 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 - An open community platform for bioimage informatics

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