News categories

sort results by

General news

( NEWS)

Software updates

( NEWS)

Cloud updates

( NEWS)

Conferences

( NEWS)

Publications

( NEWS)
23.03.2016 I Workshop on Imaging Mass Spectrometry with SCiLS Lab software training from 29-31

WIMS 2016: 1st Workshop on Imaging Mass Spectrometry with SCiLS Lab software training in Saint-Malo from 29-31 March 2016.

Only a few days left until the 1st Workshop on Imaging Mass Spectrometry in Saint-Malo starts. The Workshop focuses on practical courses and hands-on trainings directed to experts and beginners in the field of Imaging Mass Spectrometry. Users and interested persons of SCiLS Lab have the chance to participate in an interactive software training organized by SCiLS.

Participation in the software training requires registration for the workshop which is possible in a few days via
the workshop website: http://www.wims.fr.

08.03.2016 I Registration still open for the interactive software training after the Bruker User Meeting
01.03.2016 I SCiLS presented recent results on automated tumor typing of tissue sections
22.02.2016 I Service release for our MALDI imaging software SCiLS Lab 2015b available for download
16.02.2016 I SCiLS participates at MSACL 2016 US in Palm Springs, CA
11.02.2016 I Register for the interactive software training subsequent to the Bruker User Meeting in Kassel
08.02.2016 I Project meeting of the EU Horizon 2020 project METASPA CE at ICL in London
05.02.2016 I Service release for our MALDI imaging software SCiLS Lab 2015b available for download
20.01.2016 I These researchers recently used SCiLS Lab to publish scientific results in journals
20.01.2016 I OurCon IV announced: Application and Development of mass spectrometry imaging
SCiLS Lab 2019b released including new quantitation module

SCiLS Lab receives a major upgrade to version 2019b and is available for download to all users of SCiLS Lab and SCiLS Lab MVS. Users with licenses in the Pro or Premium 3D product lines will have access to the new quantitation module available with this release.

This major upgrade provides the following new features and improvements:

  • New Feature: Absolute Quantitation (Pro & Premium 3D)
    • 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

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 support@scils.de.

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 support@scils.de to learn about your upgrade options. 

Service Release for SCiLS Lab Core / SCiLS Lab Pro (Version 2019a)

A service release is available for SCiLS Lab and SCiLS Lab MVS, version 2019a of the Core, Pro and Premium 3D product lines. The following features were added to the software:

  • 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.

Your SCiLS Lab should detect the installer for this update automatically, you can also get the most recent version from our downloads section.

Service Release for SCiLS Lab Core / SCiLS Lab Pro (Version 2019a)

An important service release is available for SCiLS Lab and SCiLS Lab MVS, version 2019a of the Core, Pro and Premium 3D product lines. The following features were added to the software:

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

Your SCiLS Lab should detect the installer for this update automatically, you can also get the most recent version from our downloads section.

Service Release for SCiLS Lab Core / SCiLS Lab Pro (Version 2019a)

A service release is available for SCiLS Lab and SCiLS Lab MVS, version 2019a of the Core, Pro and Premium 3D product lines. The following features were added to the software:

  • 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.

Your SCiLS Lab should detect the installer for this update automatically, you can also get the most recent version from our downloads section.

SCiLS software workshops at ASMS 2018

The 66th ASMS Annual Conference takes place in San Diego, CA, USA from June 3-7. Like ASMS 2017, SCiLS will again contribute with software workshops. Register here and secure your free-of-charge three-month trial of SCiLS Lab.

METASPACE survey

The METASPACE online platform has been developed in the European project METASPACE and it enables the automatic metabolite annotation of mass spectrometry imaging data.

By now, more than 2000 data sets have been uploaded and analyzed by the METASPACE platform. With the following survey, we would like to learn about your experience with the platform to further improve features, usability and performance.

If you have experience with METASPACE, please complete our survey. It should not take longer than 5 minutes.

 

SCiLS contributes to Mass Spec and Proteomics, Osaka (MSP 2018)

The MSP 2018 is a joint conference of the Japanese Proteomics Society 2018 Conference (JPrOS 2018), the 9th Asia-Oceania Human Proteome Organization (AOHUPO), and the 66th Annual Conference on Mass Spectrometry, Japan.

SCiLS contributes to the conference with a talk given by Jan H. Kobarg on “Data analysis approaches for mass spectrometry imaging”.  SCiLS‘ contribution is the keynote talk is in the session „Current trends in imaging mass spectrometry“ organized by Shuuichi Shimma (Osaka Univ.) and Nobuhiro Zaima (Kindai Univ.).

 

 

Major upgrade for SCiLS Lab / SCiLS Lab MVS available

SCiLS Lab offers a multitude of tools for analysis of mass spectrometry imaging data. The 2019 version of SCiLS Lab and SCiLS Lab MVS is now available for download and included in all licenses of the Core, Pro, or Premium 3D product lines.

This major upgrade provides the following new features and improvements:

  • Revision of m/z image generation and handling to intuitive behavior
  • New blend images mode for easy creation of RGB images of multiple m/z images
  • Revision of colormaps to perceptually correct versions and new default option
  • Improved and simplified control of color gradients with new colorbar design that is manageable by visualization settings
  • Decoupled image views in stack view and tile view for displaying single images and multiple images more intuitively
  • New scalebar design with less obtrusive appearance that is manageable by visualization settings
  • Performance gain for displaying ion images from many measurements
  • Performance gain for assigning of attributes to many regions
  • … as well as numerous 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 support@scils.de.

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 support@scils.de to learn about your upgrade options. 

Recent Publications from SCiLS Lab’s Customers

In 2017, SCiLS Lab has yet again seen extended usage in papers published by the scientific community. The following articles might be of interest to you to see how SCiLS Lab has been used by other scientists:

Please contact the authors for more informations or personal copies of their papers. If you have used SCiLS Lab in your publication we would like to hear about it. Feel free to write contact@scils.de to let us know.

Service Release for SCiLS Lab Core / SCiLS Lab Pro (Version 2018b)

A service release is available for SCiLS Lab and SCiLS Lab MVS, version 2018b of the Core, Pro and Premium 3D product lines. The following features were added to the software:

  • 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

Your SCiLS Lab should detect the installer for this update automatically, you can also get the most recent version from our downloads section.

Please note: For backward compatibility, the bugfix „Reading MRMS raw data which was created with the newest ftmsControl“ has also been included in the legacy-version SCiLS Lab 2016b.

Open Webinar: Feature Extraction with SCiLS Lab

Mass spectrometry imaging produces highly complex data that is difficult to access and understand.

This webinar demonstrates feature extraction with principal components and advanced visualization techniques in SCiLS Lab.

This recording is directed to interested customers already familiar with the basic concepts of SCiLS Lab: Learn to master our powerful analysis and visualization software in this webinar.

Date: 6 March 2018 / 17 CET / 11 EST / 8 PST
Speaker: Dr. Jan H. Kobarg, Product Manager SCiLS Lab

Webinar: 6 March 2018

Access the recording of the SCiLS Lab Software Webinar.

Service Release for SCiLS Lab Core / SCiLS Lab Pro (Version 2018b)

A service release is available for SCiLS Lab and SCiLS Lab MVS, version 2018b of the Core, Pro and Premium 3D product lines. The service release fixes several minor bugs.

Your SCiLS Lab should detect the installer for this update automatically, you can also get the most recent version from our downloads section.

Service Release for SCiLS Lab Core / SCiLS Lab Pro (Version 2018b)

A service release is available for SCiLS Lab and SCiLS Lab MVS, version 2018b of the Core, Pro and Premium 3D product lines. The following features were added to the software:

  • 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

Your SCiLS Lab should detect the installer for this update automatically, you can also get the most recent version from our downloads section.

Service Release for SCiLS Lab Core / SCiLS Lab Pro (Version 2018b)

A service release is available for SCiLS Lab and SCiLS Lab MVS, version 2018b of the Core, Pro and Premium 3D product lines. The following features were added to the software:

  • 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

Your SCiLS Lab should detect the installer for this update automatically, you can also get the most recent version from our downloads section.

SCiLS software workshop at WIMS II

Following the success of the first edition of WIMS in 2016, the second workshop on Imaging Mass Spectrometry (WIMS) will be held in Saint Malo, France, on April 3-5, 2018.

WIMS is not a congress but a practical course and hands-on training for both experts and beginners in the field of imaging mass spectrometry. It provides an ideal forum for discussion of imaging mass spectrometry research.

SCiLS will contribute to the WIMS II with a software workshop. Attendees of the workshop learn important workflows and see the newest features in SCiLS Lab and SCiLS Cloud.

For more info see the official conference website.

Service Release for SCiLS Lab Core / SCiLS Lab Pro (Version 2018b)

A service release is available for SCiLS Lab, version 2018b of the Core, Pro and Premium 3D product lines. The following features were added to the software:

  • 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

Your SCiLS Lab should detect the installer for this update automatically, you can also get the most recent version from our downloads section.

Beginning with this release, it will be possible to contribute to the SCiLS Lab Development by submitting usage statistics for our software.

The gathered data is of technical and statistical nature and will automatically be sent to us. This service will not affect the performance of SCiLS Lab. The data will only be used to improve SCiLS Lab and will not be shared with any third party. You can turn off the usage statistics at any time.

Merry Christmas and a Happy New Year!

The SCiLS Team wants to wish you a Merry Christmas and a Happy New Year!

Thank you for using our software and providing feedback how to improve mass spectrometry imaging.

For us it has been very exciting now being part of the Bruker family and we are looking forward to the next year.

Search and filter functionality in SCiLS Cloud

SCiLS Cloud enables to upload and share data, results and insights. With more and more mass spectrometry imaging data sets being uploaded by the SCiLS Lab users, the data set overview became harder to navigate.

The latest release now allows to search the data set information and filter for specific types of data sets. For example, this allows hiding public data sets in the personal list of data sets.

Visit scils-cloud.com and browse through the mass spectrometry imaging data or log-in with your account and connect SCiLS Lab to upload data to your own personal space.

We are hiring

We are currently looking for a software developer focused on Server/Client- and Enterprise software solutions for our team located in Bremen, Germany. We looking forward for receiving your application.

SCiLS contributes to 4th Münster Conference on Biomolecule Analysis

This year’s Münster Conference on Biomolecule Analysis organized by Prof. Klaus Dreisewerd and his team focuses on imaging using MALDI mass spectrometry.

SCiLS will contribute to the conference with a talk on “Conceptual strategies for visualisation and analysis of mass spectrometry imaging data” given by Dennis Trede.

For more info see the official conference website.

Improved performance and stability in SCiLS Lab 2018b

For our products SCiLS Lab and SCiLS Lab MVS versions 2018b, a service release is available for download. It comes with an improved performance and stability as well as a more error-tolerant imzML import.

Additional information on all improvements can be found here: release notes.

Your SCiLS Lab should detect the installer for this update automatically, you can also get the most recent version from our downloads section.

Open Webinar: Data Analysis with SCiLS Lab

SCiLS Lab is the leading software for analysis of MS imaging data. Learn to master our powerful analysis and visualization software in this webinar.

In this Webinar, we introduce SCiLS Lab’s general capabilities as well as what is new with this year’s release. From interactive visualization in a single data set to comparative analysis of multiple samples.

This event is directed to both new customers and customers already familiar with SCiLS Lab: Get to know the software and its most important workflows.

Date: 21 November 2017 / 17 CET / 11 EST / 8 PST
Speaker: Dr. Jan H. Kobarg, Product Manager SCiLS Lab

 

To register for the SCiLS Lab Software Webinar, follow this link to our sign-up form: Register

Public datasets added to SCiLS Cloud

The list of public datasets has grown at SCiLS Cloud <scils-cloud.com>: You can now browse two more datasets which were created with our vendor-neutral software SCiLS Lab MVS.

These datasets have been available via the GigaScience (Oetjen et al., 2015) and Pride (Römpp et al., 2015) data archives, now added to our cloud storage, they can be explored interactively with our web service.

Furthermore, we made a new feature available at SCiLS Cloud: It is now possible to publicly share image annotations and load these without the necessity to register in advance.

Image annotation is provided to SCiLS Lab users as a distributed workflow between registered users. This allows an expert to annotate histologically stained images in microscopy resolution in their browser.

If you are a SCiLS Lab user, you can claim your personal storage space and start uploading data to SCiLS Cloud. Go to help.scils-cloud.de/ to learn how to connect your SCiLS Lab with SCiLS Cloud.

New application note on high-speed MALDI-TOF/TOF imaging available

Bruker Daltonics published a new application note on High-speed MALDI-TOF/TOF imaging of mouse brain tissue performed on intact proteins and after on-tissue digestion showing recent research in MALDI mass spec imaging and using our Software SCiLS Lab.

Click to download the ebook High-speed MALDI-TOF/TOF imaging.

SCiLS software demo workshop at OurCon V

30 August 2017

The program for the OurCon V mass spectrometry imaging conference from 25 to 28 September 2017 in Doorn is online.

SCiLS will contribute to the conference with a software demo workshop on Monday, 25 September. Attendees of the workshop learn important workflows and see the newest features in SCiLS Lab and SCiLS Cloud.

The workshop is unfortunately already fully booked, but we invite you to visit our posters or come to our booth during the coffee breaks if you are interested in SCiLS Lab and SCiLS Cloud.

Improved 3D visualization in SCiLS Lab 2018b

29 August 2017

For our products SCiLS Lab and SCiLS Lab MVS, an upgrade to version 2018b is available for download. SCiLS Lab 2018b comes with several new features, improvements and fixes; in particular an improved and faster 3D visualization.

Figure: New 3D transparency visualization of two m/z values introduced with SCiLS Lab version 2018b. The dataset contains serial sections adding up to 14,000 spectra of a squid provided by Janek von Byern, University of Vienna. The sections have been MALDI-imaged by Janina Oetjen, University of Bremen.

Additional information on all features can be found here: release notes.

Your SCiLS Lab should detect the installer for this update automatically, you can also get the most recent version from our downloads section.

We are hiring

23 August 2017

We are currently looking for a software developer for our team located in Bremen, Germany.

We looking forward for receiving your application.

Service Release for SCiLS Lab Core / SCiLS Lab Pro is available

21 August 2017

For our products SCiLS Lab Core and SCiLS Lab Pro (Version 2018a), a service release is available which adds six new features and fixes the following bugs:

  • 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

Your SCiLS Lab should detect the installer for this patch automatically, you can also get the most recent version from our downloads section.

Improved integration with the METASPACE online annotation platform

25 July 2017

For our product SCiLS Lab 2018a, a service release is available which improved the integration with the METASPACE online platform for automatic annotation. Our service release comes with the following improvements:

  • Now the data export is scheduled as a background task without locking the user interface. This also enables to batch export data.
  • The performance of the METASPACE export is significantly increased and is about 4 times faster than in previous versions.
  • When exporting data to imzML files we prevent gaps and blank lines in the image representation of the METASPACE engine.

If you have installed SCiLS Lab then the software will automatically check for updates and point out the new available service release. If you want to update manually, please go to downloads and select SCiLS Lab 2018a release.

For more info on METASPACE please also visit the website of the European project METASPACE.

The new SCiLS Cloud and SCiLS Lab software solutions, now with MultiVendor Support (MVS)

5 June 2017

SCiLS Lab is your tool of choice for deriving new insights from mass spectrometry imaging data. The most recent version SCiLS Lab 2018a is now available for download. It features statistical analysis and visualization of mass spectrometry imaging data such as:

  • 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

With SCiLS Lab you can compose, compare and analyse multiple data sets of virtually unlimited size. SCiLS Lab is able to process the following data:

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

SCiLS Lab is closely connected to SCiLS Cloud which offers additional workflows:

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

You can download the update here: SCiLS Lab 2018a.

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

New publication about organization and localization of small molecules within microbial assemblages

17 January 2017

SCiLS contributed to the following publication about organization and localization of small molecules within microbial assemblages and has been named Editor’s Pick:

Garg, N.; Zeng, Y.; Edlund, A.; Melnik, A. V.; Sanchez, L. M.; Mohimani, H.; Gurevich, A.; Miao, V.; Schiffler, S.; Lim, Y. W.; Luzzatto-Knaan, T.; Cai, S.; Rohwer, F.; Pevzner, P. A.; Cichewicz, R. H.; Alexandrov, T. & Dorrestein, P. C. (2016): “Spatial molecular architecture of the microbial community of a peltigera lichen”, mSystems, American Society for Microbiology, 1, e00139-16.

Microbes are commonly studied as individual species, but they exist as mixed assemblages in nature. At present, we know very little about the spatial organization of the molecules, including natural products that are produced within these microbial networks. Lichens represent a particularly specialized type of symbiotic microbial assemblage in which the component microorganisms exist together. These composite microbial assemblages are typically comprised of several types of microorganisms representing phylogenetically diverse life forms, including fungi, photosymbionts, bacteria, and other microbes. Here, we employed matrix-assisted laser desorption ionization–time of flight (MALDI-TOF) imaging mass spectrometry to characterize the distributions of small molecules within a Peltigera lichen. In order to probe how small molecules are organized and localized within the microbial consortium, analytes were annotated and assigned to their respective producer microorganisms using mass spectrometry-based molecular networking and metagenome sequencing. The spatial analysis of the molecules not only reveals an ordered layering of molecules within the lichen but also supports the compartmentalization of unique functions attributed to various layers. These functions include chemical defense (e.g., antibiotics), light-harvesting functions associated with the cyanobacterial outer layer (e.g., chlorophyll), energy transfer (e.g., sugars) surrounding the sun-exposed cyanobacterial layer, and carbohydrates that may serve a structural or storage function and are observed with higher intensities in the non-sun-exposed areas (e.g., complex carbohydrates).

For more information, visit the journal’s website or contact the authors of the paper.

SCiLS is now a part of Bruker’s journey

4 January 2017

We are pleased to announce that SCiLS now is a part of Bruker’s journey.

We are looking forward to continuing the work within this new framework together with you and as a part of Bruker’s global infrastructure making mass spec-based imaging more accessible.

For the complete press release please visit: Bruker News.