SCiLS Lab receives a major upgrade to version 2020b and is available for download to all users of SCiLS Lab and SCiLS Lab MVS. Included in this upgrade is access to our new feature SCiLS Lab annotation plugin for QuPath.

This major upgrade provides the following new features and improvements:

  • New Feature: CCS-Aware images
    • Added an import functionality to read data from timsTOF fleX data in TIMS mode
    • Added a control to visualize images from (m/z, 1/K0)-windows
    • Support annotated peak lists from MetaboScape 2021 with (m/z, 1/K0)-windows
  • New external tool: SCiLS Lab annotation plugin for QuPath
    • The plugin allows to export images and annotations from QuPath to SCiLS Lab
    • More information and alternative download at Bruker: QuPath to SCiLS Export*
      *Download requires an account on The download is a zip file which contains a .jar file and a quickstart where the usage is described.
  • Improvement: Extended the functionality in the peak list column to interact with multiple columns at once
  • Improvement: Decreased the time to add new columns to the peak table
  • Bugfix: Resolved a bug where the keyboard interactions with m/z images did not iterate through m/z images list correctly
  • Bugfix: Correctly handle the case when Windows partition or target directory is not writeable
  • Multiple stability improvements and bug fixes

You can download the update here: Download SCiLS Lab / SCiLS Lab MVS.

If you have any problems with SCiLS Lab or questions on data analysis please don’t hesitate to contact our software support team at

Please note: users who possess a SCiLS Lab 2D or SCiLS Lab 3D license – which were sold until mid-2017 – cannot use this upgrade. If you are interested in the newest version, you need to purchase an upgrade to convert the licenses to SCiLS Lab Core, Pro, or Premium 3D. Get in contact to learn about your upgrade options.

SCiLS Lab 2021a released including support for mobility images from Bruker timsTOF fleX