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Opera Phenix Data management

BioFrontiers ALMC Data Management and Sharing Plan

 

The BioFrontiers Advanced Light Microscopy Core is not responsible for your data. As the User, it is your responsibility to transfer and maintain your own data. Please note:

 

  •  The microscope and analysis workstations are not backed up. As such, any critical failure may result in the loss of any and all data that were on the computer.
  • If the hard drives become too full, ALMC staff will delete data until there is sufficient space for the next User. This deletion may happen without notice.

 

 

Advised Data Storage Locations

 

There are several remote options for you to back up your data available to you. Each has their own benefits. It is recommended that you coordinate with your advisor for the best procedure for your lab. In general, the ALMC staff does not recommend using external hard drives as the data are not readily shareable nor backed up in case of disc failure. Microsoft Teams is also not advised as space is limited and, upon your departure, your data are deleted.

 

  • BioFrontiers IT (BIT)

o For BioFrontiers-affiliated researchers and JSCBB occupants

o Allows for remote and multiple user access o Contact bit-help@colorado.edu if you would like to use their services

 

  • Research Computing

o For all CU Boulder students and staff

o Allows for remote access o Contact rc-help@colorado.edu if you would like to use their services

 

  • Cloud Storage

o Google Drive, AWS, Others

 

What to Store?

 

You should always save the raw data in its native file format (i.e., .ND2). Exporting as other formats (i.e., tiff, jpeg, png) can lead to lost meta data and compressed, unquantifiable data.

 

Opera Phenix Data Backup Protocol

 

After your session, you should backup your data from the Opera Phenix. There are two main file formats for you to export your data: 1) as a TIFF series for analysis using MATLAB, ImageJ/Fiji, other programs, or 2) as an Archive file (compatible with Harmony only). The instructions for each are below.

 

  • Exporting your data does not “delete” your data from Harmony. This is done through a separate process described below.

o Note: in Harmony, “Measurements” refers to your Images

 

  • TIFF series

o The TIFF series is only for analyzing your data outside of Harmony.

§ The TIFF series cannot be reimported back into Harmony.

o Settings -> Data Management -> Export Data

§ Method

  • Measurements Including Associated Files
  • This will be your TIFF series

 

  • Archive

o The Archive is used as a true backup of your data.

§ Archive files can be reimported back into Harmony for future analysis.

o Settings -> Data Management -> Write Archive

§ Select the measurement files you wish to archive

§ Select the destination path

  • It may be a good idea to create a separate folder per experiment or per project to help you organize your archives
  • Over time, you can add more data to an existing archive. When you import the archive, you can select the data you wish to import, so not the full archive

o Once you have archived your data, please delete the data as described below

 

 

Opera Phenix Data Deletion Protocol

 

Once you have backed up/transferred your data off Harmony, please delete your exported data from the User Data folder and your raw data through Harmony.

 

  • Delete Data from Harmony

o Settings -> Data Management -> Delete Data

§ Delete your Measurements only. The other files (experiment, analysis) can remain as these do not consume much space.

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