News
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Thomas Awarded Eurographics Dirk Bartz Prize for Visual Computing in Medicine for Cytosplore20 May 2019More...
During the Eurographics 2019 Conference, which took place in Genova, Italy, from May sixth to tenth, Thomas was awarded the Dirk Bartz Prize for Visual Computing in Medicine for his work on the Cytosplore Project. The work was submitted in collaboration with Nicola Pezzotti, Elmar Eisemann, and Anna Vilanova from TU Delft and Vincent van Unen, Na Li, Frits Koning, and Boudewijn Lelieveldt from LUMC
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Cover Image for Nature Immunology19 Feb 2019
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Study on CD4+ T Cell Variety in the Human Fetal Intestine Published in Nature Immunology21 Jan 2019More...
Our collaborators from the Immunohematology and Blood Transfusion department at LUMC published their study showing that memory CD4+ T cells are generated in the human fetal intestine in Nature Immunology. The extensive study integrates data from several sources, such as Suspension Mass Cytometry, Imaging Mass Cytometry, RNA sequencing and TCR sequencing to paint a wholistic picture of CD4+ T cells in the prenatal immune system. Particularly, the study identifies T cells with wide-ranging degrees of maturity. “The great thing is that whichever way we looked at them, all the results pointed in the same direction: the T cells are already fairly mature. They looked like mature cells and behaved that way too,” explains Van Unen.
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LCBC at SFN 20189 Nov 2018More...
Ahmed and Mandy attended the Society for Neuroscience Annual Meeting (Neuroscience 2018) in San Diego, California between 3 and 7 November. Mandy presented a poster on identifying gene expression signatures underlying stress resilience in the brain.
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LCBC at ECCB 201814 Sep 2018More...
LCBC was strongly present at ECCB2018. Marcel, Ahmed, Arlin, and Tamim represented LCBC at ECCB2018, taking place in Athens, Sep 8 to 12 this year. Arlin presented a poster on her work on identifying gene expression patterns correlated to Parkinson’s disease progression (unpublished work) and Tamim presented his method for automatic identification of cell types in mass cytometry single cell data (preprint).
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LCBC proud to be partner in DC4Balance26 Jul 2018More...
On behalf of the LCBC, Dr. Erik van den Akker will be a partner in a recently Health~Holland funded project “DC4Balance”. This project aims to develop vaccines that will restore the balance of disturbed immune systems typically observed in allergies or auto-immune diseases.
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Indu Khatri receives Marie-Sklodowska-Curie LEaDing Fellows20 Jul 2018More...
Indu Khatri has been awarded the prestiguous Marie-Sklodowska-Curie LEaDing Fellows Project. From August 20187 onward she will work for a 2-year period on “A computational model to assess vaccine efficacy based on the analysis of B-cell clonal lineages”.
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LCBC at ISMB 201827 Jun 2018More...
Marcel and Thomas will represent LCBC at ISMB conference, taking place in Chicago, July 6 to 10 this year. Thomas will give a talk in the BioVis COSI on July 9th in the first Session at 11:50 a.m. He will present an overview of the Nature Communications paper Visual Analysis of Mass Cytometry Data by Hierarchical Stochastic Neighbor Embedding Reveals Rare Cell Types, discussing HSNE and Cytosplore. Please check the full BioVis program for details.
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Online Talk on Single Cell Analysis using Cytosplore28 Mar 2018More...
Last week, Thomas gave a remote talk at the Institute of Computer Graphics of the Johannes Kepler University, Linz on the work of the group on Exploration of Large Single-Cell data with Cytosplore and HSNE. The talk has been recorded and is available on YouTube.
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Paper on Duchenne muscular dystrophy receives prize from Prinses Beatrix Spierfonds12 Jan 2018More...
Nathalie Doorenweerd from the Radiology Department at LUMC has received the annual prize of neuromuscular disease research (Jaarprijs Neuromusculaire Ziekten) from the Princes Beatrix Spierfonds.
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Single cell HSNE paper published in Nature Communications27 Nov 2017More...
We are excited to announce that our paper Visual Analysis of Mass Cytometry Data by Hierarchical Stochastic Neighbor Embedding Reveals Rare Cell Types, previously available on BiorXiv has been published in Nature Communications. The paper describes the application of HSNE, a hierarchical SNE-based technique that allows the exploration of datasets too large for other SNE-based techniques (such as t-SNE) through a hierarchical representation, to single cell mass cytometry data. See the movie below for an exemplary exploration of a dataset consisting of 5 Million cells.
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Paper on Duchenne Muscular Dystrophy is out17 Oct 2017More...
Our paper on Duchenne muscular dystrophy is published in Scientific Reports. The paper provides a comprehensive analysis of the expression patterns of dystrophin isoforms across human brain development uisng data from the Allen Brain Atlas, the Roadmap Epigenomics Consortium, and the FANTOM5 project. The results provide new insights into the cognitive phenotype associated with Duchenne muscular dystrophy.
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Leiden CBC at IEEE VIS Conference19 Sep 2017More...
Thomas will be at the IEEE VIS Conference, taking place in Phoenix, AZ from October 1st to 6th this year. He will present his latest paper CyteGuide: Visual Guidance for Hierarchical Single-Cell Analysis on Thursday, October 5th in the InfoVis Papers Session Trees and Table Tennis (10:30AM-12:10PM, room 301-D). The talk we start at approximately 11:45AM. Furthermore Nicola Pezzotti will present joint work on DeepEyes: Progressive Visual Analytics for Designing Deep Neural Networks (Wed, Oct 4th, 11:45AM, room 301-C) For the full conference program check the official program pdf.
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Ahmed featured in a Data Story from the Allen Institute10 Jul 2017More...
The Allen Institute for Brain Science released a Data Story about the work of Ahmed Mahfouz, amongst others discussing how Ahmed and our colleagues at Delft University of Technology and Leiden University Medical Center developed the open-source data visualization tool BrainScope, which was built on publicly available human brain data from the Allen Institute.
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Leiden CBC organizes a Single Cell Analysis meeting4 Jul 2017More...
On September 21, we are organizing the BioSB HotTopics Meeting on Single Cell Analysis at LUMC, with the aim of bringing together researchers with shared interest in single cell analysis. The meeting will feature presentations from the following speakers:
- Lude Franke (UMC Groningen)
- Thomas Höllt (LUMC/TU Delft)
- Patrick van den Berg (Leiden University)
- Mauro Muraro (Hubrecht Institute)
Check the full program and register here
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Keynote and Highlight Talk at BioVis 20171 Jul 2017More...
We will present our work at ISMB/ECCB and BioVis from 21st to 25th of July.
On 24th of July, Boudewijn Lelieveldt will present some of our work, including Cytosplore, in his keynote Visual Analytics for Spatial Transcriptomics: From Single Cell to Tissue and Back. Later on the same day, Sjoerd will give a Highlight Talk on his NAR paper; Brainscope: Interactive Visual Exploration of the Spatial and Temporal Human Brain Transcriptome. Both talks are part of BioVis. -
Leiden CBC at Keystone Single Cell Omics Meeting1 May 2017More...
We’ll be at the Keystone Single Cell Omics Meeting in Stockholm from May 26 to May 30 this year. Tamim will present a poster about his work on combining CyTOF marker panels and Thomas will demo our latest advances in integrating HSNE into Cytosplore.
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Ahmed receives BioSB Young Investigator 20174 Apr 2017More...
The selection committee of the BioSB Young Investigator Award 2017 has selected CBC faculty member Ahmed Mahfouz as this year’s award winner! Ahmed will receive the prize of € 500 at the annual Dutch Bioinformatics & Systems Biology conference. The award ceremony and the honorary lecture will take place on April 4 at the congress center De Wereld in Lunteren.
