SCiLS Lab Software – Changelog

SCiLS Lab 2024b 12.01.16059 (2024-04-08):

• Visualization of high and medium resolution optical images
  • When zooming in, optical images are now visualized in their original resolution in the stack view.
  • Digital microscopy images from several vendors can now directly be imported as optical images. All image data formats offered by OpenSlide 4.0.0 are supported.
  • High-resolution optical images previously coregistered in flexImaging are taken over when importing the flexImaging dataset into SCiLS Lab.
  • Large, conventional optical images are no longer stored inside a SCiLS Lab dataset, but kept as external images using a multi-resolution image format for efficient, interactive, full resolution rendering.
  • When transferring histological annotations from QuPath to SCiLS Lab, a reference to the full resolution optical image is maintained.
  • New configuration option for image visualization tile cache in SCiLS Lab Setting
  • Note: Optical images of type BMP are no longer supported. Please convert such images to TIFF or PNG.
• New coregistration workflow
  • New two-step coregistration workflow allows more intuitive and more accurate manual alignment of optical images.
  • Interactive coregistration supports up to three anchors to accommodate for non-rigid (affine) distortions.
• Managing external file references
  • Spectra source data information moved to objects tab, consistent to how external image references are handled.
  • Source data information included for non-Bruker data (requires MVS license)
  • File locations of external files (source data, external optical images) maintained in the objects tab in a consistent manner.
• Data import and storage
  • New option to perform T-ReX feature finding during import of TIMS, QTOF, or MRMS data
  • Integrity check when importing imzML data is now performed more efficiently during spectra import (requires MVS license).
  • New menu command to optimize disk space occupied by SCiLS Lab data set files
  • Storing SCiLS Lab files on external drives no longer supported by default for drives formatted using an inherently unsafe file system (exFAT and FAT32).
    Note: It is recommended to reformat these drives using NTFS. Make sure to backup any data before formatting. See SCiLS Lab User Manual for further information.
  • Better error handling during import
  • Better clean up when shutting down SCILS Lab
• CCS enabled imaging
  • In the spectrum view, CCS features are now distinguished from m/z features by a diamond marker.
  • T-ReX³ feature finding on TIMS data now takes into account the imported m/z range (instead of the full acquisition range).
• Further improvements and bug fixes
  • Changed mouse / keyboard interactions in the stack view: Right mouse (RM) click moves field of fiew, Shift-RM rotates.
  • Improved usability of spectrum list panel in the visualization tab, now consistent to ion image list.
  • External intensity features now supported in all tools (including co-localization, ROC and hypothesis test, LDA)
  • Default interval processing mode when creating a new normalization to an m/z feature now consistent with setting in file properties
  • Improvements and bug fixes related to UI rendering on large, high-dpi monitors
• SCiLS API
  • Information on optical images includes paths to external, full resolution images and corresponding transformation matrices.
  • File format definition for region and image import / export incluedes references to external image files.
  • Full support for external intensity features
  • API no longer allows writing non-finite intensity values.
  • Added binary package for Python 3.12
  • Binary package for R 4.1 removed

SCiLS Lab 2024a 12.00.15110 (2023-08-07):

• Metaboscape molecular annotation
  • Metaboscape molecular annotation is now directly accessible from the SCiLS Lab feature table
  • Target list annotation methods configured in Metaboscape can be selected to provide molecular annotations to a SCiLS Lab feature list
  • Multiple annotation candidates can be reviewed and managed in the new feature table annotation details view
  • Isotope patterns are extracted by the T-ReX feature finding and are used to provide more accurate annotations
  • Access to Metaboscape server is configured through the SCiLS Lab Settings dialog
  • Target list library “TargetList_N-Glycan human” has been updated to be compatible with the Metaboscape molecular annotation workflow
  • Notes: Requires Metaboscape 2023b or later. Separate Metaboscape and Metaboscape REST API licenses required.
    Molecular annotations currently limited to the Metaboscape “Target list” annotation tool
• Multiomics imaging
  • Ion images transferred using the SCiLS Ion Image Mapper are now represented in the destination dataset as a new type of features, external intensity features
  • External intensity features don't carry explicit m/z or mobility information, but are identified by their names
  • Normalization is not applied to such external intensity features
  • External intensity features can be used in most tools and plots, including box, ROC, and correlation plots, as well as co-localization tool, segmentation, and component analysis
  • External intensity features are supported in exports to CSV and OME-TIFF
  • An application shortcut to the SCilS Ion Image Mapper is now directly available from the user's desktop
• Improved import of timsTOF fleX TIMS mode data
  • The TDF library for accessing timsTOF fleX raw data was updated to a new version, allowing to import TIMS mode data at a higher accuracy, in particular with respect to low intensity signals
  • Note: It is not recommended to combine TIMS mode data imported with the new TDF library with TIMS data that has been imported with an earlier version of SCiLS Lab. If you need to combine multiple timsTOF fleX TIMS datasets, please consider re-importing the data using the latest SCiLS Lab version.
• Improved support for timsTOF fleX calibration information
  • SCiLS Lab now maintains the information on the active mass calibration at the time of import and makes sure consistent data is used when later accessing the timsTOF fleX raw data to perform feature finding, extract CCS images or re-generate the CCS heatmap
  • The calibration source file that was current at the time of importing the timsTOF fleX data is now stored with the SCiLS Lab dataset and can be re-created by exporting it from the Objects tab
• Further improvements and bug fixes
  • Successful execution of background tasks and certain other events are no longer signaled by notification pop-ups
  • Adding intensity columns to the feature table is now performed in a background task, thus allowing to continue working even in extreme cases where this operation may take more than a few seconds
  • Added a context menu command to delete name entries for a selection of multiple features in the feature table.
  • Fixed a bug where references to original Bruker raw spectra may have been incorrect in special cases where a new, secondary SCiLS Lab dataset was created from a subregion of an existing SCiLS Lab dataset that was created from a measurement including multiple measurement regions with different raster width settings.
    Note: It is recommended to recreate the secondary SCILS Lab dataset in such cases.
  • Polarity information now stored correctly when importing from another SCiLS Lab dataset or from non-Bruker data (requires MVS license)
  • Arrow up and down keys are now handled correctly in the ion image list
  • The intensity box plot now supports Copy to clipboard on systems with screen scaling other than 100%
• SCiLS API
  • Deprecated binary package for Python 3.7 was removed.
  • Added binary package forR 4.3. R 4.1 is now deprecated, will be removed in the next release.

SCiLS Lab 2023c 11.02.14724 (2023-05-16):

• Fixed a bug which could cause a crash on startup in some network configurations

SCiLS Lab 2023c 11.02.14721 (2023-05-03):

• Fixed a bug which prevented import of Bruker axial-tof data from dat files in some cases
• Fixed a bug that lead to crash when importing corrupted data from slx files
• Fixed a bug that could lead to a crash when instead of the data folder the parent folder was selected as data source

SCiLS Lab 2023c 11.02.14706 (2023-04-18):

• Importer improvements and automation
  • The importer now automatically detects the import project type from the selected source data
    Note to MVS users: When importing from Waters data, select one of the .INF files included in the Waters data folder.
  • Import summary improved in the case where many warnings occurred during import
• CCS enabled imaging
  • Quantitation now supports mass-mobility features
• Other feature enhancements
  • If multiple identical licenses are available, SCiLS Lab now selects a license automatically during startup without showing the license dialog
• SCiLS API improvements
  • API server automatically picks available pro license
  • New API function to add columns to the feature table
• Bug fixes
  • Fixed a bug in the CCS heatmap generation where the heatmap would be displaced in m/z direction under certain circumstances
    Note: For existing datasets, SCiLS Lab may suggest recreating the heatmap. It is recommended to recreate the heatmap in such cases to ensure highest accuracy.
  • Fixed a bug where extraction of CCS images failed for datasets where spectra were skipped during import
  • Fixed a bug where the spatial relation to the original source data was incorrect for datasets that were imported from a subregion of an existing SCiLS Lab dataset
  • Fixed a bug in the feature finding that would cause SCiLS Lab to crash under rare circumstances

SCiLS Lab 2023b 11.01.14623 (2023-02-22):

• New 3D and 4D feature finding for Bruker QTOF, TIMS and MRMS data
  • Feature finding for TIMS data based on the T-ReX³ algorithm
  • Feature finding for Bruker QTOF and MRMS data based on the T-ReX² algorithm
• Importer improvements and automation
  • Running the importer no longer blocks the main SCiLS Lab application
  • Increase importer performance by storing temporary data in a dedicated location / local SSD
  • Polarity mode is automatically determined during import
  • New command line importer enables automatic data import after acquisition
  • Improved handling of I/O errors during import
• CCS enabled imaging
  • Support mass-mobility features in computing classification models (LDA)
  • Create custom normalizations to reference mass-mobility features
  • Default mobility width can now be configured in File Properties
• Multiomics workflow, SCiLS Ion Image Mapper (prototype)
  • Support source and target data sets with multiple samples or measurement areas
  • Support mass-mobility features in multiomics workflow
  • Generate automatic names for unnamed features transferred to a target data set
• Multiple feature enhancements
  • Export feature list ion images as standard OME-TIFF files
  • Manage list of original data sources from which a SCiLS Lab file was created
  • Custom normalizations can now be deleted in the Objects tab
  • Automatic closing of data sets opened from a network location can now be configured
• SCiLS API improvements
  • New API function to write custom normalizations
  • New API function to retrieve filename and UUID of current file
  • Added binary package for Python 3.11. Python 3.7 is deprecated, will be removed in the next release.
  • Removed binary package for R4.0
• Multiple bug fixes
  • When importing centroided data (e.g., MRMS, TIMS, QTOF) and reducing the m/z range for import, TIC and RMS normalizations are now computed on the reduced range instead of the full m/z range
  • Fixed a bug in the feature navigator where the mass-mobility heatmap was not rendered correctly on close zoom-in
  • Improved layout on high dpi monitors with Windows screen scaling enabled
  • Fixed a bug where very large optical images (more than 4 billion pixels) were not rendered correctly
  • Fixed a bug where network locations with very long folder names were not supported
  • Improved path handling with Unicode characters
  • Fixed a bug where non-latin encodings in .mir exports and imports were not handled correctly

SCiLS Lab 2023a 11.00.14179 (2022-09-09):

• Fixed a bug on multiscreen setups where the file menu and tooltips would appear on the wrong screen
• Update Wibu CodeMeter License service to 7.50
• Fixed a bug where the application froze when importing from a SCiLS Lab file with many complex regions
• Fixed a bug where the application stopped working when loading a corrupted image from a SCiLS Lab file

SCiLS Lab 2023a 11.00.14157 (2022-07-22):

• New Feature Navigator simplifies working with CCS enabled imaging data
  • Visualize ion mobility features in a two-dimensional mass-mobility diagram
  • Visualize the average m/z-mobility frame as a two-dimensional heat map
  • Create new ion mobility features interactively from the heat map
• More improvements for working with timsTOF fleX CCS enabled imaging data
  • Display ion mobility values in both CCS or 1/K0 representation
  • Import feature lists with ion mobility features specified as CCS
  • Improve performance of TIMS data import
• SpatialOMx
  • Support for Miralys (Ambergen) MALDI HiPLEX-IHC data
  • New SCiLS Ion Image Mapper tool for multiomics visualization and analysis (prototype)
• Multiple feature enhancements
  • Installation includes a number of pre-defined mass libraries (target lists)
  • Box plots with better y axis labeling
  • Improve performance of data import for timsTOF fleX, scimaX, and solariX instruments
  • Create backup copy of slx file before migration
  • Close datasets opened from a network drive after some period of inactivity
  • Grace period when losing connection to license server
  • License & subscription period shown more prominently on splash screen
  • Update Wibu CodeMeter License service to 7.40b
  • Further improvements for high-DPI monitors and multiple monitor setups
• SCiLS API improvements
  • Functions to read and write optical images from or to a SCiLS Lab file
  • Secure https connections between API client and remote server
  • Windows binary packages R 4.1 and R 4.2 API clients
• Multiple bug fixes
  • Adding ion images from a thresholded feature list not working properly
  • Splash screen not always shown in multiple monitor setup
  • Invalid result objects created after cancelling a component analysis task
  • Restoring bookmark with RGB blend mode disables intensity box plot and colorbar
  • Saving screenshots of all current ion images to tiff format fails
  • CSV import fails on input data with a large number of empty columns
  • Text rendered at incorrect scale when saving a screenshot with other than the default resolution

SCiLS Lab 2022b 10.01.13622 (2022-03-09):

• This version of SCiLS Lab requires at least Windows 10 Version 1607 Build 14393
• New Feature: New import workflow of feature lists
  • Universal CSV importer for reading target analyte molecules
  • Flexible assignment of CSV columns to feature table entries
  • Automatic mapping of chemical formula to m/z values
• New Feature: Improved peak area processing mode
  • The interval processing mode “Peak Area” now uses a more accurate interpolation method and is the default for new datasets that were not acquired on Bruker TOF instruments
  • For Bruker TOF instruments, the default is “Peak Maximum” (previously named “Maximum Value on Interval”)
  • For backwards compatibility, the former peak area mode is still available as “Peak Area (legacy)”; the interval processing mode “Mean Value on Interval” is now deprecated, but still available as “Mean (legacy)”
• Further improvements for work with mobility-resolved features
  • Improved compression of files generated from timsTOF fleX data
  • Enabled using recalibrated data for timsTOF fleX data
  • Integrated image generation for mobility-resolved data into new import workflow
  • Aborted image generation can be continued at later point to generate missing mobility images
• Multiple miscellaneous feature improvements
  • Improved interface options to create columns of spectral data in the feature table
  • Responsive user interface layout to react to monitor scaling
  • SCiLS Lab annotation plugin for QuPath made compatible with QuPath 0.3 (plugin version 1.3 is included in the installation directory of SCiLS Lab)
  • Limit ion image rendering to available memory or at most 1000 images
  • Harmonized all API calls that work with ion images from the feature table
  • For imzML files without proper pixel size description, error is raised and file is rejected
  • Fixed a bug where legacy graphics cards with only OpenGL 1.1 support were not correctly recognized to use software rendering mode instead

SCiLS Lab 2022a 10.00.13102 (2021-12-10):

• Fixed a bug where switching to the 3D view could reference a not existing object
• Fixed a bug where selecting entries from the spot image list could reference a not existing object
• Fixed a bug where PCA could no longer be computed with the mean spectrum setting

SCiLS Lab 2022a 10.00.13097 (2021-09-30):

• New Feature: Improved feature table (formerly named peak table)
  • The feature table lists both m/z features and mobility-resolved features (CCS features) from timsTOF fleX
  • Instantly visualize a selected feature from the feature list as the active ion image, the selection is displayed in all views and plots
  • The overview columns also support mobility-resolved features
  • Mobility-resolved features can be added to the ion image list (formerly m/z image list)
• New Feature: Plots and statistical tools work with mobility-resolved features
  • Perform co-localization tool, ROC analysis, hypothesis tests, or spatial segmentation on feature lists containing mobility-resolved features
  • Perform component analysis (PCA or PLSA) on feature table and visualize in scores and loadings plot
  • ROC plots, correlation plot, and intensity box plot all work with any active ion image from the ion images list
• Performance improvements
  • Improved import performance for timsTOF fleX, solariX, and scimaX data
  • Further improvements on performance and memory efficiency
• Other improvements and bug fixes
  • Improved default mass axis settings for newly imported timsTOF fleX data
  • Improved the spectrum representation for newly imported Thermo profile data
  • Update Wibu CodeMeter to utilize all-digital license files to version 7.21a
  • Improved detection and error handling in case of invalid imzML files
  • Removed the deprecated feature Profiles
  • Fixed a bug where an all-digital Wibu license could not be used on a license server
  • Fixed a bug leading to an inaccurate optical image registration under certain circumstances
  • Fixed a bug where the required disk space was overestimated, preventing storing some files
  • Various other bug fixes and improvements
• SCiLS Lab API improvements
  • Added easy-to-use installation scripts for Python and R clients
  • Added an auto-migrate option for the API server
  • Added the unit tests for the API clients to ease verification of successful installation
  • Modified the API versioning scheme to better reflect compatibilities between server and client scripts
  • Fixed bugs where get_ion_images and get_spectra_matrix functions were not working correctly under certain circumstances

SCiLS Lab 2021c 9.02.12704 (2021-07-01):

• Improvement: When importing CCS images, m/z and mobility window widths provided in feature list are used (CSV file, e.g. from TIMS Data Viewer)
• Improvement: The dialog for importing CCS images remembers its mobility window width setting
• Fixed a bug where SCiLS Lab could not validate an all-digital license or connect to a license server
• Fixed a bug where the line width in the plots was not updated
• Fixed a bug where the peak list export to CSV was not using the appropriate numerical precision

SCiLS Lab 2021c 9.02.12682 (2021-05-07):

• New Feature: Native support for Waters data format*
  *Requires a SCiLS Lab MVS license
  • Supports .RAW data created with Waters HDI software
  • Allows reading data comprised of single measurement function
  • Separate interim-export to the imzML format no longer necessary
• New Feature: Native support for Thermo Fisher Scientific data*
  *Requires a SCiLS Lab MVS license
  • Supports .raw data created by MALDI imaging sources of the following types: MALDI ImageQuest, MassTech AP-MALDI, TransMIT AP-MALDI, Spectroglyph MALDI Injector
  • Allows reading MS order 1 experiments
  • Separate interim-export to the imzML format no longer necessary
• Improvements to SCiLS Lab API
  • Precompiled binary wheels for Python 3.8 and Python 3.9 have been added to the distribution
  • Source packages for the Python and R client packages provided to enable usage under Linux versions
  • Added documentation to use API client with remote server
• New Feature: Apply automatic pressure compensation on timsTOF fleX data, in particular relevant for long-running measurements
• New Feature: Additional license provider powered by Wibu-Systems
• Improved user interface for configuration of mass axis parameters during import
• Improved performance for loading spot image groups and CCS images
• Multiple bug fixes

SCiLS Lab 2021b 9.01.12514 (2021-01-26):

• New Features in the SCiLS API
  • New method to write generic spot images with fixed value ranges and ability to display them in SCiLS Lab
  • New method to write spot images with fixed RGB value for each pixel and ability to display them in SCiLS Lab
  • Multiple new use cases in the API documentation folder
  • Harmonized multiple API function calls
  • Reduced vulnerability of API usage
  • Multiple bug fixes
• Updated external tool: SCiLS Lab annotation plugin for QuPath increased to version 1.2 (included in the installation directory of SCiLS Lab)
  • Added support to load existing SCiLS Lab annotations into QuPath
  • Added support to utilizate QuPath’s TMA-dearrayer for automated tissue microarray annotation
  • Minor bug fixes
  • More information and alternative download at Bruker: QuPath to SCiLS Export*
    *Download requires an account on bruker.com. The download is a zip file which contains a .jar file and a quickstart where the usage is described.
• Improvements and bug fixes in SCiLS Lab:
  • Speed-up of reading data from timsTOF fleX and support for internal calibration
  • Improvement: Size restriction of background image now linked to memory available on graphics card
  • Improvement: Color gradient for m/z images now allows fine-tuning for the selected color
  • Bug fix: Correctly clean-up empty peak lists

SCiLS Lab 2021a 9.00.12376 (2020-10-21):

• 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 bruker.com. 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

SCiLS Lab 2020b 8.01.12082 (2020-07-27):

• Improvement: Peak lists and peak list column data are now listed in objects tab
• Improvement: Profile data is always displayed as profile spectra in spectrum plot
• Improvement: Harmonized the add m/z images and overview spectra dialogs
• Bug fix: Avoid loading data multiple times when concatenating individual data files
• Bug fix: Re-enabling opening of data files with empty peak lists

SCiLS Lab 2020b 8.01.12038 (2020-07-14):

• New Feature: SCiLS Lab API
  • Access to SCiLS Lab files via session management
  • Data access via interfaces for Python and R
  • Example workflows documented via R vignettes and Jupyter notebooks
• Improved the estimate for default peak interval width
• Improved the usability of the intensity box plot
• Multiple bug fixes and stability improvements
• Bugfix: Fixed rare crash during import or file loading introduced with version 8.01.12036 (2020-07-13)

SCiLS Lab 2020b 8.01.12036 (2020-07-13):

• Release candidate for SCiLS Lab 2020b

SCiLS Lab 2020a 8.00.11942 (2020-05-28):

• Improvement: Exports to imzML are now adapted to new peak lists
• Bugfix: Resolved a graphics card conflict after activation of the overview map
• Bugfix: Resolved failure to detect graphics card during start-up
• Bugfix: Fixed region references in spectrum names for timsTOF fleX QTOF data
• Bugfix: Resolved a rare inconsistency when columns were re-ordered in the peak table

SCiLS Lab 2020a 8.00.11756 (2020-03-02):

• New Feature: Allowing peak lists to be exported into text files for import into spreadsheet software
• New Feature: Enabling re-ordering of columns in peak list table
• New Feature: Supporting limited set of characters from scientific notation and non-Latin (Chinese, Japanese, Korean, etc.)
• Improvement: Simplified user interface and distinction of tables
• Improvement: Increased performance when handling with long peak lists
• Improvement: Avoid storage of m/z images when no data is available to display
• Multiple bug fixes and stability issues related to loading external data into existing SCiLS Lab files

SCiLS Lab 2020a 8.00.11593 (2020-01-13):

• Improvement: Import and export of peak lists from peak table
• Improvement: Faster creation of timsTOF fleX data
• Bugfix: Resolved missing initialization of active m/z value in some tools
• Bugfix: Resolved pagination in tile view error
• Bugfix: Resolved MetaboScape workflow not working for combination of multiple files
• Novel external tool for peptide MALDI imaging data that allows to re-calibrate SCiLS files
  • The tool implements the approach from the recently published a paper on recalibration of peptide MALDI imaging data (Boskamp et al., Anal Chem. 2019).
  • The tool only works on peptide data measured on axial TOF instruments.
  • More information and download at Bruker: SCiLS Align Peptides*
    *Download requires an account on bruker.com. The download is a zip file which contains a small .exe file and a readme.txt file where the usage is described.

SCiLS Lab 2020a 8.00.11549 (2019-12-05):

• New Feature: Annotation of peak lists
  • Assign names to peaks in SCiLS Lab
  • Transfer annotated peak lists from one SCiLS Lab file to another
  • Import annotated peaks from other software like MetaboScape 5.0
  • Perform calculations on annotated peak lists and propagate results more easily
  • Summarize results from statistical analysis more easily in the new peak list table
• New Feature: Automated annotation of metabolites, lipids, and glycans together with MetaboScape 5.0 for SpatialOMx
  • Molecular annotation of measured ions can be performed together with MetaboScape 5.0 (separate product)
  • The workflow combining SCiLS Lab and MetaboScape automatically matches measured ions to molecular information in metabolomics, lipidomics, and glycomics workflows.
  • The workflow supports Bruker’s MRMS platforms scimaX and solariX, as well as the timsTOF fleX
• New Feature: Support of Bruker timsTOF fleX data
  • Support of the QTOF file format .tsf
  • Support of the timsTOF file format .tdf per m/z projection
• New Feature: New concept for single ion image generation and blended multiple ion image generation
• Improvements:
  • Simplified m/z image handling
  • Simplified spectrum view controls
• Multiple bugfixes

SCiLS Lab 2019c 7.02.10980 (2019-05-02):

• Missing mean spectra are calculated also when attribute editor is closed
• Report table shows notification if selected mean spectra do not exist

SCiLS Lab 2019c 7.02.10975 (2019-04-09):

• New Feature: Added “Peak Area” as new interval processing mode
• Improvement: Better performance when importing, and working with, centroid data
• Improvement: Better performance for region attributes in large data sets
• Improvement: Reworked the tile view for better handling and performance
• Improvement: Temporary files get deleted as soon as a task is finished
• Bugfix: Fixed several bugs in the intensity box plot to increase stablility
• Bugfix: Fixed denoising bug which produced holes in some circumstances
• Bugfix: Fixed colorbar bug which did not update the m/z value when the image is unchanged
• Multiple minor bugfixes

SCiLS Lab 2019c 7.02.10901 (2019-02-21):

• Improvement: Better coloring of centroid data with a lot of zeros in the m/z images
• Bugfix: Could not open files with “.” in their names from importer
• Bugfix: m/z image generator was slow
• Bugfix: Changes of thresholds in m/z intervals were not stored in some cases

SCiLS Lab 2019c 7.02.10879 (2019-02-08):

• Major stability and performance improvements
  • Rework of internal data handling to improve general performance
  • SCiLS Lab is now using two files to store the data and extended information separately
  • Separate cache for tools to increase data integrity
  • Editing of region attributes accelerated
• Multiple minor bugfixes

SCiLS Lab 2019b 7.01.10764 (2018-11-08):

• Bugfix: Fixed crash when canceling a non running scheduled task.

SCiLS Lab 2019b 7.01.10759 (2018-09-25):

• New Feature: Absolute Quantitation
  • Define calibrant regions with different concentrations
  • Compute and visualize calibration curve
  • Assess fit to data and limits of quantitation
  • Calculate quantity for unknown regions
• New feature: Easy-to-use m/z value selection field that suggests m/z values from already loaded m/z images
• Improvement: Improved the performance of MRMS profile data import
• Improvement: Mass axes are stored with higher numerical precision
• Several minor bugfixes and performance improvements

SCiLS Lab 2019a 7.00.10623 (2018-08-24):

• Improvement: Less memory consumption when importing datasets with many regions.
• Improvement: Error messages for incorrect imzml files contain less confusing debug information.
• Improvement: Normalizations are calculated with higher numerical precision.
• Bugfix: Empty imzml datasets are detected correctly and are rejected to be imported.
• Bugfix: Some machines were unable to validate license correctly.

SCiLS Lab 2019a 7.00.10534 (2018-08-06):

• New feature: Provide possibility to create a cleaned sl file with reduced size.
• Bugfix: Fixed detection of write protected files from network drives.

SCiLS Lab 2019a 7.00.10514 (2018-07-11):

• Bugfix: Fixed bug which made file grow significantly in size. Should fix some performance issues.

SCiLS Lab 2019a 7.00.10513 (2018-07-04):

• Bugfix: Increased SL file cache. Should fix some performance issues.

SCiLS Lab 2019a 7.00.10512 (2018-06-29):

• New feature: SCiLS Lab now reads content from files that were not correctly closed or marked as broken, and tries to create a repaired file.
• Improvement: “Normalization to Peak” is now added by on-the-fly control instead of tool.
• Improvement: Speed-up the import of spectra into sl files.
• Bugfix: Failed to show 3D image when the dataset was registered only partially.
• Bugfix: Ignore empty spectra during imzML export.
• Bugfix: Failed to load huge images or many individual m/z images.

SCiLS Lab 2019a 7.00.10446 (2018-05-23):

• Bugfix: Storing regions from labels when no class was selected.

SCiLS Lab 2019a 7.00.10445 (2018-05-15):

• Bugfix: Loading m/z images with partial 3d registration.

SCiLS Lab 2019a 7.00.10443 (2018-05-02):

• New feature: Revision of m/z image generation and handling to intuitive behaviour.
• New feature: New blend images mode for easy creation of RGB images of multiple m/z images.
• New feature: Revision of colormaps to perceptually correct versions and new default option.
• New feature: Improved and simplified control of color gradients with new colorbar design that is manageable by visualization settings.
• New feature: Decoupled image views in stack view and tile view for displaying single images and multiple images more intuitively.
• Improvement: New scalebar design with less obtrusive appearance that is manageable by visualization settings.
• Improvement: Performance gain for displaying ion images from many measurements.
• Improvement: Performance gain for assigning of attributes to many regions.
• Deprecated feature: Removed lower quantile from settings.
• Bugfix: Preserve import projects on error during importing process if temporary files cannot be accessed or deleted.
• Bugfix: Creation of 3D objects could crash the program if no file was loaded.
• Bugfix: Report table now displays inherited attributes correctly for sub-regions.
• Bugfix: Segmentation of imzML data could use up memory if too many blank pixel were used.
• Bugfix: Zoom level could be set to infinite and now has reasonable limits.

SCiLS Lab 2018b 6.01.10220 (2018-03-16):

• Feature: Region report table can display standard deviations of m/z images.
• Improvement: Added some tooltips for menu buttons in the region attribute editor.
• Bugfix: Reading MRMS raw data which was created with the newest ftmsControl.
• Several minor bug fixes

SCiLS Lab 2018b 6.01.10198 (2018-02-16):

• Bugfix: Loading some old bookmarks crashed SCiLS Lab.
• Bugfix: Double click on back button in importer sometimes crashed SCiLS Lab.

SCiLS Lab 2018b 6.01.10194 (2018-02-02):

• Improvement: When saving regions the proposed color is randomly chosen.
• Bugfix: Crash when two instances were checking the same security dongle at the same time.
• Bugfix: Some tif images were displayed with a wrong alpha channel. Images were too dark or too light.
• Bugfix: When opening a new file, the current m/z images can be retained.
• Several minor bug fixes

SCiLS Lab 2018b 6.01.10183 (2018-01-19):

• Feature: Support new dat format generated by new flexControl versions.
• Improvement: Report table displays some values in FT datasets with higher precision.
• Bugfix: Rare crash when creating an m/z image with an interval outside of the data.
• Bugfix: 3D-Registration with large images was not working properly.
• Several minor bug fixes

SCiLS Lab 2018b 6.01.10174 (2018-01-08):

• Feature: Users can provide anonymous statistical data to improve SCiLS Lab
• Improvement: Performance of datasets with many regions (Region tree interactions, animation performance)
• Improvement: Importer uses less memory for FT data
• Improvement: SCiLS Lab is closing faster
• Several minor bug fixes

SCiLS Lab 2018b 6.01.10065 (2017-11-17):

• Improvement: Tools are checking the needed memory and give a comprehensive message
• Bugfix: Screenshots might have had slightly different resolution than on screen
• Bugfix: Open file from folders containing special characters by double click in windows explorer
• Bugfix: Exception after upgrading a dongle on start dialog, when leaving the dialog whithout a selected dongle
• Bugfix: OpenGL error showing black widgets on some systems
• Bugfix: Icons could not be loaded on some systems
• Bugfix: Several minor bug fixes

SCiLS Lab 2018b 6.01.9996 (2017-11-07):

• Improved performance and stability
  • Improved performance for giant data sets
  • Improved performance for data sets containing comprehensive regions’ meta data
  • New optimized file structure which significantly grows less while performing data analysis
  • More frequent progress reporting preventing time-outs of SCiLS Lab
  • Improved startup process of SCiLS Lab. Progress reporting when opening and closing an .sl file
  • Checking available main memory before executing computational tasks as, e.g., ROC
  • Faster startup of the 3D registration module
  • Driver check for incompatible NVIDIA Quadro display adapters with outdated hardware drivers. In this case a software rendering engine will be used instead of hardware rendering.
• Improvements of multi-vendor support
  • More robust of imzML import by means of improved automatic error correction
• Improvements of the importer
  • Improved tiling of multiple measurement
  • Importer keeps the order of imported measurements
  • Bugfix: The overview image was one pixel off in the optical image coordinate system
  • Bugfix: Loading .sip files sometimes had wrong behavior
• Bugfix: Quota codes for SCiLS Cloud
• Bugfix: Several minor bug fixes

SCiLS Lab 2018b 6.01.9932 (2017-09-26):

• Improvement: Performance for files with many regions
• Bugfix: AUC values might differ between tool “Find discriminative m/z values (ROC)” and ROC curve graph due to numerical instabilities
• Bugfix: Crash when closing scils lab after mean spectrum tasks have been aborted
• Bugfix: Paste into attribute editor when sorted by attribute column
• Bugfix: Several minor bug fixes

SCiLS Lab 2018b 6.01.9874 (2017-09-08):

• Feature: SCiLS Lab can handle large images (flexImaging 5 compatibility)
• Feature: Added Get Pro / Get MVS entry in the Help menu for suitable licenses
• Improvement: Loading Bookmarks is faster
• Bugfix: Several minor bug fixes

SCiLS Lab 2018b 6.01.9825 (2017-08-29):

• Feature: Improved visualization by the use of a new visualization engine
  • Faster 3D visualization
  • Improved 3D volume visualization
  • Improved 3D transparency with slice visualization
  • Requires graphic adapters and drivers capabale of OpenGL 3.2
  • Added software rendering compatibility mode
• Feature: Improved the coregistration of optical images
• Feature: Improved the auto-completion in the attribute editor
• Bugfix: Elimination of a randomized component in spatial smoothing
• Bugfix: Fixed crash when moving regions containing sub-regions
• Bugfix: Could not load mis files on systems with certain codepages (e.g. Japanese Windows)
• Bugfix: Replaced GIF generator which failed on some systems

SCiLS Lab 2018a 6.00.9747 (2017-08-15):

• Feature: Hotspot removal is now executed automatically
• Feature: The gel view uses maximal contrast within the zoomed range
• Feature: All loaded m/z images can now be batch saved as jpg or png images
• Feature: imzML data is imported with a horizontal flip to conform with other softwares
• Feature: Improved search for true/false attributes in region tree
• Feature: Plotter can now combine auto y scaling with compare mode
• Bugfix: Fixed a bug where region attributes did not appear when using the labels report table
• Bugfix: Classification models imported from other sl files now correct deviations in normalization target values
• Bugfix: Fixed bug where the importer falsely reported insufficient disk space
• Bugfix: Fixed off by one error for spectrum ids in CSV export
• Bugfix: Peak picking would not run despite pressing “Yes” in warning dialog
• Bugfix: Several minor visualization bugs in the plotter
• Bugfix: Several minor bug fixes

SCiLS Lab 2018a 6.00.9673 (2017-07-19):

• Feature: Exporting data is now a background task
• Feature: Improved performance accessing spectra from FT-ICR data
• Feature: Improved import performance for FT-ICR data and from existing SCiLS Lab files
• Feature: Allowing import of imzML files with incorrect value in ibd checksum
• Feature: Allowing import of imzML files with incorrect value in ibd binary type
• Bugfix: Adding multiple columns to the report table respects the sort order
• Bugfix: Increased number of decimal places for FT-ICR profile data
• Bugfix: Fixed error handling when file is located in write protected folders like primary harddrive C:
• Bugfix: Allowing new files to be saved to Desktop
• Bugfix: Cancelling tasks executes abortion at earliest possible break
• Bugfix: Prevention of possible coordinate overlap in imzML exports
• Minor bug fixes and improvements

SCiLS Lab 2018a 6.00.9568 (2017-06-02):

• Instant visualization of ion images, spectra, and numerous statistical visualization options
• Region attributes to manage meta-information like clinical annotations or experiment settings
• Comparative analysis for uncovering discriminative m/z-markers
• Co-localization analysis for discovering correlated m/z-values
• Spatial segmentation for automatic annotation of prominent features
• Component analysis for extraction of underlying trends
• Classification model calculation based on training data and classification of new samples
• Construction, visualization and analysis of 3D models from consecutive measurements

• Native support for all major Bruker mass spectrometer
• Vendor-neutral imzML format

• Secure access with a standard web browser
• Upload and share data, results and insights
• Allow partners or team members to annotate histologically stained images