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Resources

CIPA has a close collaboration with the Swedish National Infrastructure for Computing (SNIC) and the Lund university centre for scientific and technical computing (LUNARC). Here users can apply to use large-scale computing resources for analysis and simulations. CIPA has staff to aid and assist users in accessing the SNIC and LUNARC resources and guide in every step of the way from application to finished analysis/simulation.


Below is a list of useful 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 training, support or just answer simple questions. Resources are added continuously, so make sure you keep checking back for updates!

Shortcuts

 

Analysis and tool development

The experts in CIPA can guide and aid in development and modify 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

Two workstations are currently available. The stations are primarily intended for processing cryo-EM data but can also be used for other purposes, and are available for the use of any interested Lund University users. These machines are equipped with two high end GPUs each, allowing for fast parallel processing using software like Cryosparc or Relion. In order to get access to these computers, you can contact Markel Martinez at markel [dot] martinez_carranza [at] med [dot] lu [dot] se.

Open source/free

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.

https://imagej.net

or just

https://fiji.sc/

Tutorials are available here.

CellProfiler

CellProfiler can read and analyze most common microscopy image formats as well as recognize regions of interest (cells, colonies).

Relion

Relion is an image-processing software for cryo-electron microscopy (Cryo-EM).

Scipion

Scipion is an image processing framework for obtaining 3D models of macromolecular complexes using Electron Microscopy (3DEM).

Commercial

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 here.

Collaborations

Arivis Vision4D

In collaboration with the Lund University Bioimaging Centre (LBIC), the imaging core at Lund University, CIPA can help you access the powerful imaging visualization and analysis suite Arivis. For information on booking, fees and availability click here. This license is continuously updated and so the latest version is always available.

Imaris Neuroscience

In collaboration with Multidisciplinary research focused on Parkinson´s disease (MultiPark), CIPA can help you access the Imaris neuroscience package. For information on booking, fees and availability click here.

You can also contact Jonas Ahlstedt directly for information on both programs as well as booking.

Cost of services

The services of CIPA has been free of charge during the initial start-up phase but CIPA is from the 1st of October 2021 entering next phase including introduction of user-fees. As before, initial counselling is free of charge and any support or errand lasting less than hour should not be charged. The use of the CIPA workstations will also continue to be free of charge for the users.

  • Quickly resolved issues (<1 hour) are free of charge, and no user fees are involved when contacting a CIPA member for help and/or consultation. 
  • For smaller projects (~10-20 hours) CIPA charges 325 SEK per hour (one of our experts working on the case).  
  • For any projects estimated to take longer than 20 hours, the approximate time will be calculated along with a project and cost plan as well as delivery details.