Please send us your protocol (Word, pdf) and we will upload it here.
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.
For studying host-pathogen interactions, use Imaging Flow Cytometry at the FACS Core Facility at Biomedicine.
... 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.
Come to our Open Office sessions to discuss your imaging needs or get advice on workflows, free of charge:
Or contact us on:
*) This PC has a Nvidia RTX 2070 graphics card for high performance image processing.
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.
*) This PC has an ASUS DUAL-GTX1660S-6G-EVO graphics card for high performance image processing.
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) |
This PC has a Nvidia RTX 2070 super graphics card for high performance image processing.
Fiji is ImageJ with additional plugins e.g. allowing opening of multiple file formats.
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
Go to: https://imagej.nih.gov/ij/docs/guide/146.html
In order to open Olympus (.vsi) files, please follow this guide:
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 – Image Batch Processing and Data Analysis
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
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.
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) - 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
OpenCV - an open source computer vision and machine learning software library.