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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
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.

Season Greetings from SCiLS

19 December 2016

The entire team from SCiLS wants to thank you for a wonderful year 2016 and sends out greetings of the season and best wishes for a Merry Christmas and Happy New Year!

weihnachtskarten2016

Service Release for SCiLS Lab 2016b is available

7 December 2016

For our product SCiLS Lab 2016b, a service release is available which fixes the following bug:

  • Fixed bug where the loadings plot would not show the loadings

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

Recent Publications from SCiLS Lab’s Customers

2 December 2016

Since our summer survey, SCiLS Lab has yet again seen extended usage in papers published by the scientific community. The following articles might be of interest to you as well 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.

Survey: Imaging MS community 2016

28 November 2016

In 2015, we surveyed imaging MS community to answer the question „What imaging MS is used for?“. Thank to 111 scientists who responded, we learned much and shared the results:

summary_figure

 

Today, we would like to learn how the field of imaging MS changed since then. We created a new 2016 survey.

If you have experience with imaging MS, please complete our new 2016 survey: http://metaspace2020.eu/survey2016.

Service release for SCiLS Lab 2016b available for download

28 November 2016

A service release for SCiLS Lab 2016b is available for download. It comes with the following changes:

  • Fixed bug where segmentation would run endlessly.

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 2016b release.

New publication about automated metabolite annotation

22 November 2016

SCiLS contributed to the following publication about automated metabolite annotation in high-mass-resolution imaging mass spectrometry:

Palmer, A.; Phapale, P.; Chernyavsky, I.; Lavigne, R.; Fay, D.; Tarasov, A.; Kovalev, V.; Fuchser, J.; Nikolenko, S.; Pineau, C.; Becker, M. & Alexandrov, T. (2016): “FDR-controlled metabolite annotation for high-resolution imaging mass spectrometry”, Nature Methods, advance online publication.

High-mass-resolution imaging mass spectrometry promises to localize hundreds of metabolites in tissues, cell cultures, and agar plates with cellular resolution, but it is hampered by the lack of bioinformatics tools for automated metabolite identification. We report pySMSM, a framework for false discovery rate (FDR)-controlled metabolite annotation at the level of the molecular sum formula, for high-mass-resolution imaging mass spectrometry. We introduce a metabolite-signal match score and a target–decoy FDR estimate for spatial metabolomics.

For more information, visit the METASPACE2020.eu consortium website or contact the authors of the paper.

Plenary talk by Theodore Alexandrov at EMIM 2017

15 November 2016

Theodore Alexandrov, scientific director of SCiLS GmbH, team leader at the Structural and Computational Biology Unit, European Molecular Biology Laboratory, and Assistant Adjunct Professor at Skaggs Schoolf of Pharmacy, University of California San Diego, will hold a plenary talk at the 12th European Molecular Imaging Meeting – EMIM 2017 in Cologne, Germany on 7 April 2017.

For more information see the website of the 12th European Molecular Imaging Meeting – EMIM 2017.

Service release for SCiLS Lab 2016b available for download

11 November 2016

A service release for SCiLS Lab 2016b is available for download. It comes with the following changes:

  • Improved storing and loading speed of large bookmarks
  • Improved initialization for co-registrating images
  • Improved stability of importer with implausible or duplicate content in .mis files
  • Improved logging and incident handling
  • Improved consistency in the 3D registrator for alternative reference images
  • Bookmarks will now tell the user if they were recorded with different file settings and adjust them accordingly
  • Reduced needed disk space for importing large datasets
  • Fixed reset of camera view in the 3D mode when new objects are not visible
  • Fixed unintended visual behavior in 3D when changing the denoising state of m/z images
  • Fixed cancelling of the import
  • Fixed Import when .mis files contains areas with the same name
  • Fixed next/previous peak behavior in non-sorted peak lists

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 2016b release.

Service release for SCiLS Lab 2016b available for download

7 November 2016

A service release for SCiLS Lab 2016b is available for download. It comes with the following changes:

  • Reduced memory consumption during import
  • Improved import speed for certain large datasets
  • Added support for different raster sizes in one .mis file when importing from DAT
  • Added warning when opening files from network or removable devices
  • Fixed several smaller bugs for the 3D visualization
  • Fixed bug which reset the layout in the importer after saving an import project
  • Fixed bug which could lead to an 1 pixel offset for optical images
  • Improved time reporting of the batch importer
  • Improved stability of the batch importer
  • Improved and extended logging
  • Fixed importer crash when data contains garbage spectra
  • Improved general stability

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 2016b release.

Service release for SCiLS Lab 2015b available for download

7 November 2016

A service release for SCiLS Lab 2015b is available for download. It comes with the following changes:

  • Added warning when opening files from a removable or network drive.

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 2015b release.

Raf Van de Plas speaks at Bremen Mass Spectrometry Seminar

24 October 2016

On behalf of the Bremen Mass Spectrometry Seminar SCiLS invites you to attend this month’s lecture:

Raf Van de Plas (Delft University of Technology / Delft Center for Systems and Control)

Integrating Mass Spectrometry with Other Imaging Technologies: Improving Biological Insight Through Data-driven Multi-modal Image Fusion

Medical studies increasingly employ a multitude of different imaging technologies to answer a specific biological question. A growing number of such multi-modal imaging studies include Imaging Mass Spectrometry (IMS) as one of these modalities. Although different modalities are routinely registered and overlaid to generate a single display, true integration of data across technologies is largely left to human interpretation, resulting in a significant underutilization of the potential of multi-modal measurements. This talk gives an overview of our recent work on the integration or ‘fusion’ of IMS with measurements from other imaging modalities, and demonstrates the potential of data-driven image fusion for IMS through several predictive applications. Example applications include: (i) the ‘sharpening’ of IMS images, using microscopy measurements to predict ion distributions at a spatial resolution that exceeds that of measured ion images by ten times or more; (ii) the enrichment of biological signals and the removal of instrumental noise by multi-modal corroboration; and (iii) the prediction of ion distributions in tissue areas that were not measured by IMS. We also highlight more recent work in which, contrary to fusing IMS with microscopy, our data-driven fusion method is used to combine two mass spectrometry-based modalities into a single predicted modality that combines advantages of the source modalities. In this new IMS-IMS fusion setting, MALDI-TOF IMS (high spatial resolution, limited mass resolution) is fused with MALDI-FTICR IMS measurements (lower spatial resolution, higher mass resolution), enabling ion distributions to be predicted with both high spatial as well as high mass resolution. Examples are shown in lipid imaging, where there is both a need to spatially resolve fine tissue structure, as well as a need for high chemical specificity due to nominally isobaric species.

Time and Date: Wednesday, 26 October 2016, 16:00 at the Max Planck Institute for Marine Microbiology (new lecture hall)

There will be a small reception with wine and cheese after the seminar. For more information about the seminar and upcoming speakers, please visit www.bremen-ms-seminar.de/.

Introducing SCiLS Cloud and Service Releases for SCiLS Lab

14 October 2016

SCiLS is proud to present a new product in our portfolio: SCiLS Cloud. SCiLS Cloud is a web service which enables you to upload and share data, results and insights.

You are invited to visit https://scils-cloud.de and register an account.

If you are using our MALDI imaging software SCiLS Lab, version 2015 or version 2016, a service update is available for you. These service updates provide support to link your SCiLS Lab with SCiLS Cloud and allowing you to upload data into the cloud. Learn more about the connection between SCiLS Lab and SCiLS Cloud in our Cloud Help Center.

Dashboard of SCiLS Cloud

New version SCiLS Lab 2016b is available for download

8 September 2016

An update for our MALDI imaging software SCiLS Lab is available for download. New functionality and several improvements have been added, thanks to the valuable feedback from our users. The features include

  • Improved usability for FT-ICR data analysis
    • When importing multiple SQLite data sets a consolidated peak list is generated during import
    • Improved visualization of mean spectra for SQLite data
  • Official interface to METASPACE alpha version
    • Ability to export data to the official METASPACE engine delivering molecular annotations
  • Improved visualization for plots and graphs
    • Possibility to adjust the line thickness
    • Possibility to adjust the font size
  • Numerous improvements and fixes such as
    • More robust hot spot removal when using the median normalization
    • Improved behavior of the tools Find co-localized m/z values and Find discriminative m/z values when working on peak lists
    • More stable behavior of the objects tab
    • More stable behavior when importing .sl files
    • Fixed a volume rendering bug for the SCiLS Lab 3D version
    • Fixed a rendering bug which prevented showing regions twice in SCiLS Lab 3D
    • Hundreds of small improvements and fixes

You can download the update from our downloads page. If you have any problems with SCiLS Lablike questions on data analysisor are interested in upgrading from earlier versions of SCiLS Lab, please don’t hesitate to contact our software support team at support@scils.de.

Service release for SCiLS Lab 2015b available for download

25 August 2016

A service release for SCiLS Lab 2015b is available for download. It comes with the following changes:

  • Minor Bugfixes

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 2015b release.

Two new papers are available online to which SCiLS contributed

10 August 2016

SCiLS contributed to the following publications:

Abstract: Histopathological subtyping of non-small cell lung cancer (NSCLC) into adenocarcinoma (ADC) and squamous cell carcinoma (SqCC) is of utmost relevance for treatment stratification. However, current immunohistochemistry (IHC) based typing approaches on biopsies are imperfect, therefore novel analytical methods for reliable subtyping are needed. We analyzed formalin-fixed paraffin-embedded tissue cores of NSCLC by Matrix-assisted laser desorption/ionization (MALDI) imaging on tissue microarrays to identify and validate discriminating MALDI imaging profiles for NSCLC subtyping. 110 ADC and 98 SqCC were used to train a Linear Discriminant Analysis (LDA) model. Results were validated on a separate set of 58 ADC and 60 SqCC. Selected differentially expressed proteins were identified by tandem mass spectrometry and validated by IHC. The LDA classification model incorporated 339 m/z values. In the validation cohort, in 117 cases (99.1%) MALDI classification on tissue cores was in accordance with the pathological diagnosis made on resection specimen. Overall, three cases in the combined cohorts were discordant, after reevaluation two were initially misclassified by pathology while one was classified incorrectly by MALDI. Identification of differentially expressed peptides detected well-known IHC discriminators (CK5, CK7), but also less well known differentially expressed proteins (CK15, HSP27). In conclusion, MALDI imaging on NSCLC tissue cores as small biopsy equivalents is capable to discriminate lung ADC and SqCC with a very high accuracy. In addition, replacing multislide IHC by an one-slide MALDI approach may also save tissue for subsequent predictive molecular testing. We therefore advocate to pursue routine diagnostic implementation strategies for MALDI imaging in solid tumor typing.

Abstract: A standardized workflow for matrix-assisted laser desorption/ionization imaging mass spectrometry (MALDI imaging MS) is a prerequisite for the routine use of this promising technology in clinical applications. We present an approach to develop standard operating procedures for MALDI imaging MS sample preparation of formalin-fixed and paraffin-embedded (FFPE) tissue sections based on a novel quantitative measure of dataset quality. To cover many parts of the complex workflow and simultaneously test several parameters, experiments were planned according to a fractional factorial design of experiments (DoE). The effect of ten different experiment parameters was investigated in two distinct DoE sets, each consisting of eight experiments. FFPE rat brain sections were used as standard material because of low biological variance. The mean peak intensity and a recently proposed spatial complexity measure were calculated for a list of 26 predefined peptides obtained by in silico digestion of five different proteins and served as quality criteria. A five-way analysis of variance (ANOVA) was applied on the final scores to retrieve a ranking of experiment parameters with increasing impact on data variance.

 

New SCiLS Lab Publications from our Customers

29 July 2016

Our software SCiLS Lab was used by numerous customers to create a vast number of scientific publications in research journals. The following articles might be of interest to you as well 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 2016a available for download

4 July 2016

A service release for SCiLS Lab 2016a is available for download. It comes with the following changes:

  • m/z correlation table now reacts to region changes accordingly

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 2016a release.

Webinar on high-resolution MALDI imaging

15 June 2016

SCiLS participates in a webinar discussing high-resolution MALDI imaging organized by Bruker.

The webinar titled “Uncovering Metabolic Pathways in Disease to Support Drug Discovery Using High Resolution MALDI Imaging Mass Spectrometry” takes place

June 16, 2016

8:00 a.m. PDT / 11:00 a.m. EDT / 16:00 BST / 17:00 CEST

Speakers are Dr. Jan H. Kobarg, Product Requirement Manager at SCiLS, and Dr. Ellen Jones, Research Scientist at the MALDI Imaging Research Center at Genentech.

Visit the c&en website for more information and registration details.

Release of SCiLS in the Cloud: www.scils-cloud.de

14 June 2016

During the ASMS Conference on Mass Spectrometry and Allied Topics, SCiLS released an alpha version of the software component SCiLS Cloud which allows to share MALDI imaging data together with results of statistical analysis in the web.

After computational analysis with SCiLS Lab, users have the ability to upload results to SCiLS Cloud. Data together with analysis results such as discriminative m/z-markers uncovered by comparative analysis or regions of interest resulting from spatial segmentation or from tissue classification can be shared with collaborators and viewed in a web browser.

An alpha version of SCiLS Cloud is available together with some example data sets at www.scils-cloud.de. We are looking forward to receiving your feedback.

Release and upload of own data is planned for fall 2016.

The following system requirements apply:

  • Our web-based application works in modern browsers as, e.g., Mozilla Firefox or Google Chrome.
  • Desktop or laptop computer are supported only. Mobile devices such as smartphones or tablets are not supported yet.
  • 3D-capable graphics card with minimal screen resolution 1680×1050.
  • Broadband internet connection.

alpha_SCiLSInTheCloud

SCiLS participates at the 64th ASMS Conference on Mass Spectrometry and Allied Topics in San Antonio, Texas

2 June 2016

The ASMS Conference on Mass Spectrometry and Allied Topics is attended by more than 6,500 scientists. Approximately 3,000 papers are presented as posters and talks. The 64th ASMS Conference takes place in San Antonio, Texas, on June 5 – June 9, 2016.

SCiLS contributes to the following talks and posters

  • “FDR-controlled metabolite annotation for high-resolution imaging mass spectrometry”, talk given by Theodore Alexandrov. Monday, June 6, 2:50pm – 3:10pm, Hemisfair 3.
  • Parallel untargeted and targeted quantitative metabolomics for microbiome research, Poster 208
  • Software for distributed MALDI imaging workflows, Poster 246
  • Comparative mapping of PSA and N-glycan distributions in FFPE prostate cancer tissues using MALDI-FTICR and rapid MALDI-TOF Mass Spectrometry Imaging, Poster 318
  • MALDI Imaging a tool for clinical diagnostic – classification of prostate cancer subgroups, Poster 320
  • Automated tumor typing of tissue sections based on characteristic spectral patterns extracted from MALDI mass spectrometry imaging data, Poster 375
Service release for SCiLS Lab 2016a available for download

04.05.2016

A service release for SCiLS Lab 2016a is available for download. It comes with the following changes:

  • Improved visual feedback in importer when importing region hierarchies
  • Improved automatic determination of the minimal interval width for FT data
  • Batch importer can be triggered from start dialog
  • Batch import can be canceled during preparation phase
  • Fixed error when deleting a component analysis that is currently loaded
  • Fixed error when importing Regions that have no name
  • Minor improvements

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 2016a release.

New version SCiLS Lab 2016a is available for download

25.04.2016

We are happy to announce that a new version of our MALDI imaging software SCiLS Lab is available for download. SCiLS Lab 2016a comes with numerous new features improving productivity and expanding the scope of the applications. This, e.g., includes

  • Combine and extend .sl files
    • The importer is now able to handle SCiLS Lab .sl files
    • With this you can combine and extend .sl files with other .sl and .mis files
    • The possibility to import smaller subsets of .sl and .mis files
  • New batch import
    • The new batch importer is able to import several measurements into individual SCiLS Lab .sl files
    • Each resulting .sl file corresponds to one individual measurement (.mis file); all .sl files are generated by the same settings
    • The batch importer works self-sufficiently in the background, so you can keep working with SCiLS Lab
  • Import / Export of regions
    • You can export regions from one data set and import it into another one
    • This enables to use distributed workflows together with your peers
  • Improved usability and visual feedback
    • Improvement of interactivity and representation of regions
    • The region tree is more intuitive with selecting and editing
    • The cursor in the spectrum view now snaps to the closest peak
  • Faster data visualization
    • Faster creation of ion images from peak lists
    • Faster refreshing of ion images after adjusting visualization parameters, e.g. the normalization options or the denoising level
  • Hundreds of small improvements and fixes

 

You can download the update from our downloads page. 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.

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

23.03.2016

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.

Registration for SCiLS Lab software training on 15 March 2016 in Kassel, Germany

08.03.2016

As previously announced, subsequent to the Bruker Mass Spectrometry User Meeting 2016 in Kassel, SCiLS organizes a half-day, interactive software training with the current SCiLS Lab version 2015b. This provides an effective way to learn typical use cases for MALDI imaging data analysis and the handling of our software SCiLS Lab.

Participation in this workshop is free. Contact us for more information: support@scils.de.

Automated tumor typing of tissue sections based on MALDI mass spectrometry imaging data and machine learning using characteristic spectral patterns

01.03.2016

The MSACL 2016 US, the 8th Annual Conference on mass spectrometry applications to the clinical lab took place in Palm Springs, California on February 21–25, 2016. SCiLS presented recent results on automated tumor typing of tissue sections.

  1. Boskamp, D. Lachmund, J. Oetjen, R. Casadonte, J.H. Kobarg, J. Kriegsmann, P. Maass. Automated tumor typing of tissue sections based on MALDI mass spectrometry imaging data and machine learning using characteristic spectral patterns. (download)

We present an automated classification method for MALDI mass spectrometry imaging data with applications to tumor typing of FFPE tissue sections. The proposed method consists of a) data pre-processing, b) identification of characteristic spectral patterns using non-negative matrix factorization (NMF), and c) applying linear discriminant analysis (LDA) for classification. We apply this method to the discrimination of breast, lung, colon and pancreas cancer. MALDI data has been acquired from eight tissue micro arrays (TMAs), two for each tumor type, with a total of 943 cores from 285 patients. Four TMAs have been used for training, the remaining four TMAs for validation. A sensitivity on core level of 100.0% (lung), 99.5% (pancreas), 100.0% (colon), and 100.0% (breast) was achieved. Only limited effects of different preprocessing variants (normalization, filtering) were observed.

NEWS_ABSTRACT

Service release for SCiLS Lab 2015b available for download

22.02.2016

A service release for SCiLS Lab 2015b is available for download. It comes with the following bug fixes:

  • Reduced file size for FT-ICR data
  • Improved FT import process

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 2015b release.

SCiLS participates at MSACL 2016 US in Palm Springs, CA

16.02.2016

The MSACL Conference provides a forum for discussion of developments in the clinical application of mass spectrometry. The 8th Annual Conference MSACL 2016 US will be held in February 21 – 25, 2016 in Palm Springs, CA.

SCiLS participates with a poster presentation on „Automated tumor typing of tissue sections based on MALDI mass spectrometry imaging data and machine learning using characteristic spectral patterns“ given by Tobias Boskamp.

The abstract reads as follows:

We present an automated classification method for MALDI mass spectrometry imaging data with applications to tumor typing of FFPE tissue sections. The proposed method consists of a) data pre-processing, b) identification of characteristic spectral patterns using non-negative matrix factorization (NMF), and c) applying linear discriminant analysis (LDA) for classification. We apply this method to the discrimination of breast, lung, colon and pancreas cancer. MALDI data has been acquired from eight tissue micro arrays (TMAs), two for each tumor type, with a total of 943 cores from 285 patients. Four TMAs have been used for training, the remaining four TMAs for validation. A sensitivity on core level of 100.0% (lung), 99.5% (pancreas), 100.0% (colon), and 100.0% (breast) was achieved. Only limited effects of different preprocessing variants (normalization, filtering) were observed.

SCiLS Lab software training on 15 March 2016 in Kassel, Germany

11.02.2016

Subsequent to the Bruker Mass Spectrometry User Meeting 2016 in Kassel, SCiLS organizes a half-day, interactive software training with the current SCiLS Lab version 2015b. This provides an effective way to learn typical use cases for MALDI imaging data analysis and the handling of our software SCiLS Lab.

Participation in this workshop is free. Contact us for more info and registration details: support@scils.de.

METASPACE: Project meeting of European project on Bioinformatics for Spatial Metabolomics

08.02.2016

Partners of the EU Horizon 2020 project METASPACE have met at Imperial College London to discuss the progress in the project. The project’s main goal is to develop novel algorithms for the annotation of high-resolution mass spectrometry imaging. For further information, check out the METASPACE project website.

Service release for SCiLS Lab 2015b available for download

05.02.2016

A service release for SCiLS Lab 2015b is available for download. It comes with the following bug fixes:

  • Fixed offset in some tissue profile mode data sets
  • Fixed display of plots computed on m/z intervals
  • Improved error reporting of tools if no data for an m/z interval is available

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 2015b release.

SCiLS Lab used in new publications in scientific journals

20.01.2016

SCiLS is proud to see our software SCiLS Lab is used by our customers to successfully publish their research in notable journals. The following articles might be of interest to you as well to see how SCiLS Lab has been used by other scientists:

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.

Date and place of OurCon IV, 4th Imaging Mass Spectrometry Conference announced

20.01.2016

The organizers of the OurCon IV have just announced the time and date for the fourth conference dedicated to the application and development of mass spectrometry imaging:

Dear friends and colleagues,

On behalf of the organizing committee we are delighted to welcome you to OurCon IV, a
conference dedicated to the application and development of mass spectrometry imaging. The
conference will be held in Ustron, Poland, on October 17th-21st, 2016.

The conference subjects will include MSI methodology, 3D-MSI, MSI bioinformatics, multimodal
imaging, clinical MSI, pharmacological MSI and new applications. The program also includes
dedicated time for late breaking news and young researcher contributions through a “Young
Guns” session.

The OurCon series has quickly established itself as one of the major annual events in the field
of mass spectrometry imaging. Previous conferences were organized in Ourense (2012),
Antalya (2014) and Pisa (2015). OurCon IV will also be the inaugural meeting of the newly
founded Mass Spectrometry Imaging Society, a non-for profit society dedicated to the promotion
of mass spectrometry imaging and its widespread application.

We look forward to welcoming you in Ustron!

On behalf of the conference organizers:

Piotr Widlak
Local organizing committee

Liam A. McDonnell
MSIS

More information will be available soon at www.ourcon.org. The registration will open on March 1, 2016.

MaDiPath: Kick-off meeting

18.01.2016

The partners of the project MaDiPath met at SCiLS for kick-off. In the project funded by the Federal Ministry of Education and Research (BMBF), Germany, mass spectrometry imaging is used for questions of clinical pathology. The projects deals with the development of standard operating procedure (SOP) von clinical routine workflows and the development of novel computational tools for pathology based on MALDI imaging.

The project duration of MaDiPath is from October 2015 to September 2018 and the project consortium unites the following partners from academia and industry:

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

11.01.2016

SCiLS will participate in the 1st Workshop on Imaging Mass Spectrometry in Saint-Malo. The Workshop focuses on practical courses and hands-on trainings directed to experts and beginners in the field of Imaging Mass Spectrometry. During this event SCiLS organizes a half-day, interactive software training with the current SCiLS Lab version 2015b.

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.

SCiLS Lab software training on 15 March 2016 in Kassel, Germany

11.01.2016

Subsequent to the Bruker Mass Spectrometry User Meeting 2016 in Kassel, SCiLS organizes a half-day, interactive software training with the current SCiLS Lab version 2015b. This provides an effective way to learn typical use cases for MALDI imaging data analysis and the handling of our software SCiLS Lab.

Participation in this workshop is free. Contact us for more information: support@scils.de.