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Resources

Research Infrastructures and Initiatives

Examples of research infrastructures of high relevance for the CIPA community, at Lund University and elsewhere (external links):

Through the National Academic Infrastructure for Super¬≠computing in Sweden (NAISS) and the Lund University centre for scientific and technical computing (LUNARC), CIPA users can apply for, and access from any location, storage as well as large-scale computing resources for analysis, visualization and simulations. CIPA has staff to aid and assist users in accessing the NAISS and LUNARC resources and to guide them in every step of the way from application to finished analysis/simulation.

CIPA is actively collaborating with other Research Infrastructures at the Lund University local level, including the BioSAXS unit at the Center for Scattering Methods, MBio, LBIC and LUNARC.

Analysis and Tool Development

CIPA offers access to e.g., Arivis Vision4D and Imaris Neuroscience. Contact the CIPA application experts directly for information on both programs and booking.

The experts at CIPA can guide and aid in development and modification of software to meet the users' needs for analysis tools. Examples include MATLAB programming for identification of cellular components, quantification and position of markers, implementing data formats in open source software, machine learning and AI for improved analysis.

Hardware

Several workstations are available for users from Lund University at BMC C14. Two of the stations are primarily intended for processing cryo-EM data but can also be used for other purposes. The stations are available to any interested user from Lund University. The cryo-EM machines are equipped with two high-end GPUs each, allowing for fast parallel processing using software like Cryosparc or Relion.

Software and Tools

Below is a list of useful resources, including software and tools for image analysis, accompanied by short descriptions and download links. If you are new to any of these programs, please contact us and we can arrange a training, provide you with support or just answer simple questions. Resources are added continuously, so make sure you keep checking back for updates!

Open Source / Free Software

ImageJ/Fiji

Fiji (Fiji Is Just ImageJ) is a fully open source image processing package based on ImageJ and comes with many bundled plugins suited for bioimaging. Read more at imagej.net or just fiji.sc.

Tutorials texts, scripts and videos are available in the online documentation: ImageJ tutorials.

CellProfiler

CellProfiler can read and analyze most common microscopy image formats as well as recognize regions of interest (cells, colonies). For more information, see the CellProfiler website.

Relion

Relion is an image-processing software for cryo-electron microscopy (Cryo-EM). Documentation and downloads can be found on the Relion website.

Scipion

Scipion is an image processing framework for obtaining 3D models of macromolecular complexes using Electron Microscopy (3DEM). The latest version can be found on the Scipion website.

Commercial software

MATLAB

A site-wide license for MATLAB by MathWorks is available for students and employees at Lund University. You can access both the software and the necessary licenses through the Software LTH website.