Image analysis tools

The Bioimaging Facility team assists in automation of image analysis workflows or establishing new image analysis routines using the image analysis programs available at I.S.T. Austria.

Scripts:

  • We provide custom tailored analysis scripts in FIJI, Matlab or python. Some examples can be found here – more information

Machine learning approaches:

  • We provide machine learning approaches, such as ilastik or C.A.R.E. – more information

Scratch: a central data processing drive

Our workstation are all connected to a network drive named ‘scratch‘ via an 10 Gb network! This allows users to process data directly on scratch. Thus copying to local workstation hard drives is not needed anymore, thereby saving you a lot of time. In addition, scratch is connected to all workstations. You do not have to book any specific workstation anymore because your data is stored on that system. You do need to check if the workstation has the specification and software that you need to perform your analysis. The scratch drive is only mounted when users log on with their own user-profile -> do not forget to log-off after your session.

You can also mount scratch ‘manually’: just copy the following address into the address bar of the file explorer and provide your IST\username credentials when prompted: \\scratch3.ist.local\scratch-bioimaging\

  • each research-group has his own folder that is only accessible by the group members
  • data that has not been re-saved for longer than 30 days will automatically be deleted

Data transfer:

  • Speed-test to any analysis workstation (or microscope) can be done using the speed-docker