Initiatives and Research Infrastructures of high relevance for the CIPA community
Through collaborations with the Swedish National Infrastructure for Computing (SNIC) 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 SNIC 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 LU local level. Through these collaborations CIPA offers access to Arivis Vision4D and Imaris Neuroscience. You can also contact Jonas Ahlstedt directly for information on both programs and booking.
Analysis and Tool Development
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.
Two workstations are currently available. 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. 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 (markel[dot]martinez_carranza[at]med[dot]lu[dot]se).
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
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.
Tutorials are available here.
CellProfiler can read and analyze most common microscopy image formats as well as recognize regions of interest (cells, colonies).
Relion is an image-processing software for cryo-electron microscopy (Cryo-EM).
Scipion is an image processing framework for obtaining 3D models of macromolecular complexes using Electron Microscopy (3DEM).