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7. Bruker TruLive3D Data management

 For questions, comments or concerns please email us at biof-imaging@colorado.edu 

Data acquired on the Bruker TrLive3D will typically be very large, on the order of TeraBytes of data. The Luxendo computer has enough internal capacity to store up to ~20TB of data. This seems like a lot of storage but we are asking the users to transfer their data to their own server/storage devices immediately after an experiment so that there is always a lot of space for the next user to save their experiment.

Data management is going to be a major challenge for working with the Bruker TruLive3D Light-sheet microscope. Please read this page carefully and plan accordingly.

Data acquisition

Option 1: Write your data locally on the Luxendo computer. This is the recommended safest option.​

  • Update the Bruker Data management Book Keeping excel sheet with your experiment settings

  • Update your own excel sheet with your experiment settings. You can use this template.​

  • Create a folder for your group in the DATA drive. ​

  • Save your data in this folder with this nomenclature: Lab_Initials_Date_DataDetails for example Anseth_KA_20230719_organoidsDay3​

  • Once the experiment is done, transfer the data to your network drive or to an external hard drive.

  • MAKE SURE YOU SAVE THE EXPERIMENT SETTINGS!!!​

  • Delete your data from the computer.​

  • Data that has not been deleted within 30 days will be deleted by facility staff. If space is needed for another experiment, facility staff will reserve the right to delete data without warnings.

Option 2: Write your data directly on your network drive. This may work for short experiments and save you the transfer process. Unfortunately, the internet is not always reliable, to avoid any interruption during a long experiment over several hours we recommend writing data on the Luxendo computer. ​

  • Update the Bruker Data management Book Keeping excel sheet with your experiment settings

  • Update your own excel sheet with your experiment settings. You can use this template.​

  • Save your data with this nomenclature: Lab_Initials_Date_DataDetails, for example Anseth_KA_20230719_organoidsDay3

  • MAKE SURE YOU SAVE THE EXPERIMENT SETTINGS!!!​

In doubt always check with facility staff about how and where you should save your data.

Data pipeline

The following diagram is the vision for future data pipeline in the Beckman Lab:

  • Acquire data on Bruker computer
  • Perform any kind of processing you want with the LuxBundle software
  • Transfer your data to your server via the 10GB ethernet line, or to your personal hard drive storage

  • Analyze your data with the Imaris workstation which will be installed next to it, with a hard wire connection.
  • Transfer your data to your server via the 10GB ethernet line, or to your personal hard drive storage

Data pipeline V1.png

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