Computational Image Analysis and Processing
Image processing is any form of signal processing where the input and output signals are images, and is commonly used to improve the signal:noise ratio and allow more accurate analysis of biological imaging data. Image analysis is the extraction of data from images and includes simple methods such as plotting intensity profiles as well as complex ones such as those used for object recognition and tracking of objects over time.
We provide project-based support to develop custom-tailored image processing and analysis workflows and routines using the image processing and analysis software packages available at the GIIF. Email firstname.lastname@example.org to request support.
There are two dedicated workstations in the imaging facility equipped with state-of-the-art image analysis software packages – both open source and commercial.
Open Source Image Processing and Analysis Packages
Fiji (Fiji Is Just ImageJ) is an open-source image processing package based on ImageJ which includes a large number of the most useful plugins available. Fiji can be used for almost any image processing or analysis task, and additional plugins can be added to enable new functions. The Imaging Facility Team can assist with finding appropriate plugins or writing custom scripts and plugins to meet your specific requirements.
CellProfiler is an open-source application designed for quantitative analysis of 2D imaging data using a pipeline construction approach.
icy is an open community platform for visualisation, annotation and quantification of bioimaging data.
BioImageXD is an open-source software package for analysing, processing and visualising multi-dimensional microscopy images. It includes versatile tools which can be built into pipelines and aims to provide a user friendly interface.
Arivis Vision 4D
Arivis Vision4D is a modular software allowing for the efficient handling of multidimensional, multi-terabyte data derived from diverse imaging modalities such as confocal and light-sheet systems. The software offers robust analysis pipelines for 3D / 4D image processing and analysis tasks, including rendering, stitching, segmentation, tracking, quantitative measurements, and statistics. Users can easily create and export 3D / 4D high resolution movies for publication.
Introduction to arivis Vision4D – https://youtu.be/4Dintro
Library of Video Tutorials – https://imaging.arivis.com/imaging-science/video-tutorials
Self-training material – https://cloud.arivis.com
The GIIF Arivis Vision4D workstation can be booked via PPMS
Huygens – LINK: https://svi.nl/Huygens-Professional
The Huygens Software provides assisted workflows for deconvolution and restoration of your image data. The software wizards allow you to restore your microscopy images without being a specialist on image restoration and optical theory.
Introduction to Deconvolution – https://svi.nl/DoingDeconvolution
Library of Video Tutorials – https://svi.nl/Webinars
The GIIF Huygens workstation can be booked via PPMS
Training requests and equipment bookings are done through PPMS