With PC1 in room 270E you can process your images using:
*) This PC has a Nvidia RTX 2070 graphics card for high performance image processing
**) 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.
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
With Image Processing PC3 in room 368 you can do:
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.
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)
*Don´t be confused! Fiji is just imageJ but with useful plugins (eg. plugins to open multiple file formats)
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)
Quick guide to co-localization in 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
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/Cell Analyst – Image Batch Processing and Data Analysis
ICY - An open community platform for bioimage informatics
OpenCV - an open source computer vision and machine learning software library.
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) - an open-source software system for 3D computer graphics, modeling, image processing, volume rendering, scientific visualization, and 2D plotting