Training in CVL and ImageJ/FIJI

Training in CVL and ImageJ/FIJI @ VIS2021

Date: 1 March, 2021 and 2 March, 2021

Time: 12:30 pm – 3:30 pm (Brisbane time) (duration 3 hours)

Instructor: Dr Nicholas Condon (UQ) and Dr Kathryn Hall (NIF)

Workshop information

Workshop 1 – 1 March, 2021 – FIJI/ImageJ within CVL

Please join with us to learn how to FIJI/ImageJ within the CVL desktop for light microscopy images.

Topics covered:

• Lattice light data
• 3D viewer
• Scripting, macros and batch processing

This is a hands-on workshop that will be hosted online.  Firstly there will be a short introductory presentation, and this will be followed by guided step-by-step procedures.  Please come ready to login to CVL and follow the steps along with Nicholas.  There will be time during and afterwards to ask questions and practice working with your own data.

****Registration is required by ASAP to allow for set-up with IT.  Please register here.****

If you do not have a CVL account or need refreshing, please contact kathryn.hall@uq.edu.au for assistance.

References:

Rueden, C. T.; Schindelin, J. & Hiner, M. C. et al. (2017), “ImageJ2: ImageJ for the next generation of scientific image data”, BMC Bioinformatics 18:529, PMID 29187165, doi: 10.1186/s12859-017-1934-z.

Workshop 1 – 2 March, 2021 – Data transfer methods

Topics covered:

• RDM to gain access to HPC (Awoonga and Wiener or Massive)
• StrudelWeb
• logging in to CVL
• transferring data using RDM, WindowsSCP and FileZilla, OMERO, CloudStor+.

This is a hands-on workshop that will prepare you to be able to commence analysing your own data from within CVL.  In order to complete the Data Transfer Training Workshop on 2 March, 2021, you must be able to log in to CVL with your own account and access your own folders.

For further information, please contact:

Kathryn Hall – kathryn.hall@uq.edu.au