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From Liebel-lab
Welcome to Liebel-Lab @ KIT - Karlsruhe Institute of Technology -
BioInterfaces Programme
Interested in a Ph.D Position? ->> BioInterfaces Gradschool - Interested in a Master position? ->> Students?
We develop scientific instruments and software tools.
Our core expertise: Next genereation High Content Screening platforms (robotic microscopes), Computer Aided Microscopy (Leica),
micro-arrays, bioinformatic data integration ("Bioinformatic Harvester"), high throughput image analysis (millions of images), lab robotics,
LabView rapid prototyping and most importantly -> fun.
Nature Methods: "Automated High Throughput mapping in zebrafish embryos"
 Zebrafish High Content Screen (magnify) |
- We analyzed 30.000 Zebrafish via High Content Screening microscopy and novel image processing methods.
- Published online: 8 November 2009 | doi:10.1038/nmeth.1396
- Automated high-throughput mapping of promoter-enhancer interactions in zebrafish embryos
- Jochen Gehrig1,2,5, Markus Reischl3,5, Éva Kalmár1,5, Marco Ferg1, Yavor Hadzhiev1,2, Andreas Zaucker1,2, Chengyi Song1,4, Simone Schindler1, Urban Liebel1 & Ferenc Müller1,2
Abstract: link to Nature Methods
- Zebrafish embryos offer a unique combination of high-throughput capabilities and the complexity of the vertebrate animal for a variety of phenotypic screening applications.
- However, there is a need for automation of imaging technologies to exploit the potential of the transparent embryo. Here we report a high-throughput pipeline for registering domain-specific reporter expression in zebrafish embryos with the aim of mapping the interactions between cis-regulatory modules and core promoters.
- Automated microscopy coupled with custom-built embryo detection and segmentation software allowed the spatial registration of reporter activity for 202 enhancer-promoter combinations, based on images of thousands of embryos. The diversity of promoter-enhancer interaction specificities underscores the importance of the core promoter sequence in cis-regulatory interactions and provides a promoter resource for transgenic reporter studies.
- The technology described here is also suitable for the spatial analysis of fluorescence readouts in genetic, pharmaceutical or toxicological screens.
Plexus BioInterfaces large scale Data integration platform (Trunov/Wezel/Christen/Liebel)
The Biointerfaces programme generates a vast amount of data in different fields.
Literally 100s of TByte (and soon Pbytes ) and Mio of files need to be stored and processed.
Flexible and transparent acces to all the data-sets is key for most BioInterfaces projects.
Instead of using a "super-Base" we develop a network of flexible data nodes.
All data nodes (image based, sequence based, NMR based etc will be indexed via the distributed search engine YaCy.
This architecture allows us to easily integrate new data projects, test new software versions or simply compare different data sources WITHOUT changing a database model.
- "Plexus" can be searched via a custom YaCy Search engine interface.
- YaCy is a distributed search engine (http://yacy.net) which uses the advantages of peer-to-peer technology.
- A Simple google-like search interface will allow the user convenient access to all data nodes.
- Individual data-viewer (e.g. OME-Omera for microscopy data) allow the user to browse the individual data sets.
- Plexus
- Currently "Plexus" is running in a prototype environment indexing some 300 Mio scientific documents on 25 standard Linux PCs
- Feel free to try the YaCy-Sciencenet prototype: http://sciencenet.fzk.de
Automatic Water immersion objective (collaboration with Leica/EMBL (Sieckmann/Winkler - Liebel)
 Leica Microsystems (magnify) |
In collaboration with Leica microsystems (Frank Sieckmann) and EMBL mechanical workshop (Sigfried Winkler), we developed (originally for the Mitocheck project)
an automatic water immersion objective. The automatic water dispenser allows long term (48h+) imaging experiments with a water objective. The dispenser cap also enables long term screening experiments with many position across a sample.
- See the Leica Microsystems webpage for details. http://www.leica-microsystems.com
- See Harvester42 for all Leica microsystems news Leica News
- Find the flyer here Automatic water objective
Features of the automatic water objective:
- No interaction required during the experiment
- Water reservoir fits in the center of the objective holder (magnetic)
- Software controlled water immersion supply
- No water damage (to the microscope) due to water protection collar
- Prevents disruption of water film during stage movement – intelligent water cap design
- Correction ring accessible -> optimal image quality
- Full free working distance available
- No separate water heating required – Water reservoir and micro pump fit into climate chamber
- Patent pending
Bioinformatic Harvester IV integrating knowledge (Kindler / Liebel)
 BioInformatic Harvester (magnify) |
"Bioinformatic Harvester IV" is a one-stop portal for major protein/gene resources.
Currently > 36 database are integrated and cross-linked.
A convenient "Google-like" search interface allows "real-time" data queries.
New Harvester IV features
- tabbed navigation allows convenient browsing
- new categories: overview,BLAST, expression,gene-view,global,
- new categories: literature, networks, products, protein domains
- new categories: sequence, special, uniprot
- New ultra fast search engine
- Web-based maintenance systems allows novel DB integration in < 5mins
- tabbed navigation allows convenient browsing
- allows gene/protein/sequence information to be cross-linked
- Try Harvester http://harvester.fzk.de
- Read the Wikipedia Harvester article for details...
Existing Harvester III features
- Integrates human, mouse, rat, zebrafish, arabidopsis and drosophila information
- Harvested information is always up-to-date (via "iframe" technology")
- Harvester serves ~10.000 pages to the scientific community every day
- Modular design: Novel databases are continuously integrated
- Static HTML pages allow easy search engine integration
- Static HTML pages allow easy project integration and collaborations
Harvester Publication: Bioinformatics. Harvester': a fast meta search engine of human protein resources. Liebel U, Kindler B, Pepperkok R. 2004 Aug 12;20(12):1962-3. Epub 2004 Feb 26.
CAM - Computer Aided Microscopy (Sieckmann(Leica) / Legradi / Gröbner / Liebel)
- Computer Aided microscopy "converts" your automated Leica microscope (SP5) to an intelligent screening microscope.
- CAM is a joint development project of Leica microsystems and KIT (started at EMBL Heidelberg (Mitocheck project)
- Various CAM software modules detect structures of interest
- e.g. mitotic cells, zebrafish structures, rare cell types (transfected cells).
- Experiments start automatically after an interesting structure/staining has been indentified.
- CAM integrates microscope, data storage systems, computing clusters and robotics in a flexible screening environment
- CAM allows very complex assay automation
- CAM features a "training interface".
- CAM allows integration of ANY image processing routine.
- CAM allows low resolution overview images + high resolution detailed analysis of biologically interesting structures in the same run.
- CAM software runs on one or several PCs within your network and communicates with microscopes in "real-time"
- CAM has an easy, human readable language that can be implemented in any programming language (LabView, Matlab, C++, C#, Java, Python etc.)
- CAM reduces data storage needs up to 90%
- CAM increases screening speed x-fold --> only interesting cells/structures are acquired
YACY Sciencenet - Search ~300.000.000 scientific webpages (Michael Christen)
 Sciencenet 300 Mio documents (magnify) |
- YaCy-Sciencenet is a distributed search engine prototype based on "peer2peer" technology (Michael Christen et al.).
Instead of copying the internet to a data-center (google approach),
YaCy peers (= PC + YaCy software) share data between the data serving machines itself.
Each YaCy-PC communicates with a network of distributed peers only if data is queried.
- Features of YaCy search engines:
- Allows indexing/searching anything from small websites to large scale data repositories
- Indexes text, images, docs, pdf, ppt etc (200 document types)
- Holds up to 1-100 Mio web pages or documents per peer
- Tested from single PC installation up to ~100 low cost PC clusters
- Requires no cooling racks (standard PCs)
- Requires less power (compared to 1 HE server units)
- Try it: http://sciencenet.fzk.de
- Challenge/goal: An independent and open search engine for scientific content.
- Status: "sciencenet-network ~300 Mio documents; "freeworld-network" ~ 10^9 documents
Harvester42 - Meta Search engine integrating 50 major search engines (Björn Kindler/ Urban Liebel)
 Harvester42 search engine (magnify) |
Harvester42 queries ~26 major internet search engine in parallel.
Harvester42 integrates the following search engines. Many of those search engines are meta-search engines themselves.
- BING
- YaCy (open source p2p search)
- Google Patents (convenient patent search)
- Google products
- PolyMeta (includes 5 major engines)
- Exalead (includesMSN,Yahoo,Ask etc)
- Scirus for scientific information
- Sciencedaily for science news
- Sciencenet our p2p distributed search engine
- Directindustry for product search
- YIF Yale Image finder
- YouTube (all in video)
- clusterpatent (for patent meta search)
- Mamma (another meta search engine)
- Bioinformatic Harvester (our bioinformatic meta search engine)
- ...and many more
Screening-Center building 341
Building 341 is almost in the center of the KIT campus (north) and an ideal place for projects,
which require expertise from several disciplines and institutes.
Building 341 is now home for:
- Bioinformatic Harvester (see above)
- Bioinformatic webservices
- YACY-Sciencenet a distributed search engine based on "peer2peer" technology
- Large scale zebrafish screening projects (Müller/Liebel)
- Large scale cell-based siRNA screening projects (Weiss)
- Large scale screening data analysis (Mikut/Reischl)
- Microarray data analysis
- ASIC-Search a novel processor design for fast genome sequence searches
- Lab automation projects
- LabView rapdid prototyping
- Screening assay / instrument development
- Screening microscope developments
- Read more in the screening-center article
Zebrafish Tox-Screen image processing (Rüdiger Alshut / Markus Reischl)
- Modern High Content Screening microscopes allow rapid image acquisition from 1000s of zebrafish embryos daily (for cell based screens see article below). We developed a platform for systematic chemical compound studies in large numbers (e.g. 10.000 - 100.000 ) of zebrafish including automated image analysis.
- A robust algorithm (currently implemented in MatLab) detects whether the fish is "unhappy" , dead or alive after several hours of compound exposure.
- The algorithms is orientation independent and therefore dechorionation or pre-orientation of the larvae is not necessary.
- The algorithm detects zebrafish acquired from standard multi-well plates and removes artefacts from the image.
- An automated artificial intelligence classifier "separates" the embryos.
- Currently the algorithm provides an accuracy (proper detection) of ~99%.
- Ongoing work: Detection of distinct phenotypes from highly heterogeneous images.
- If your are interested in running a set of tests or if you have questions please contact markus.reischl (at) iai.fzk.de
High Content Screening Image analysis (Markus Reischl)
To raise significant statistical conclusions, data from numerous digital microscopies has to be analyzed and high-throughput microscopy has become a means for raising data in a greater scale. However, data evaluation is often done manually which restricts the number of experiments to be evaluated due to time consuming processing steps.
We develop a new framework for zebrafish analysis and focus on a general approach which is not specific to a special kind of microscope, age of fish or noise distribution and give a guidance how to establish image processing for zebrafish. Our aim is the automation of the complete image analysis to drastically increase efficiency and thus, to make high throughput zebrafish microscopy possible.
The following steps have been established:
- Design of an intelligent computer vision routine that detect the embryo as well as tissues like yolk, cerebellum, notochord etc. automatically
- Implementation of an artificial intelligence to decide about the quality of the results of the computer vision routine
- Validation of the framework to prove robustness
The algorithm is in use in an experiment with 500000 images. It seeks to reveal tissue specificities of combinations of enhancers and promoters by deriving an activation index describing the YFP activity in body segments of an embryo. This is achieved by counting fluorescent pixels in the image and assigning them to body parts extracted from the computer vision routine.
Custom designed siRNA-Screen to identify Ca activated Cl channels (Semir Jeridi)
We use RNAi in an automated Screening system to identify the gene that encodes for an elusive yet very important ion channel protein. This channel protein plays an important role in the excitation of sensory neurons (e.g. pain, olfaction) and smooth muscle cells, in development, the regulation of vascular tone, epithelial fluid secretion and it has also shown to be upregulated in several cancers. Upon activation by free Ca2+ it can conduct Cl ions in either direction over the plasma membrane, depending on the electrochemical gradient.
We use a cell line derived from precursors of rat olfactory neurons to perform RNAi experiments. This cell line functionally expresses the channel protein. A list of candidate proteins to be tested in knock-down experiments was derived from a proteome analysis of the cilia of olfactory neurons. In the cilia of these neurons the channel is abundant in high concentration.
As the knock-down of the channel in our cell line should lead to a loss of the endogenous channel function, we probe for a reduction of Ca2+ dependant Cl- fluxes upon siRNA transfection. Therefore we have developed a fluorescence based assay on these cells that uses Cl-sensitive YFP as a reporter and implemented it in an automated screening system.
This System we developed uses the fully automated Olympus IX81 fluorescence microscope and combines it with several liquid handling devices, integrated and controlled by a custom designed software. It thus allows the automated addition of several agents and simultaneous measurement of fluorescence with a (sub)cellular resolution. With this method the measurement of thousands of cells per experiment is no problem, providing a reliable statistical basis.
The first candidates resulting from this screening approach are now being further investigated using the precise but extremely time and labour intensive patch clamp technique. This project is a collaboration with the group of Prof. Stephan Frings at the Department of Molecular Physiology (University of Heidelberg).
Olympus Scan^R - screening microscope
 Olympus Scan^R Screening Microscope (magnify) |
(collaboration with Olympus Europa and Olympus Soft Imaging Solutions.
We developed the Scan^R Screening station software in collaboration with Olympus. Scan^R screening microscopes can be found in many labs already and allow fully automated high quality image acquisition. Projects fom 100 - 15 Mio images have been realized on 1-4 parallel running Scan^R microscopes.
The KIT screening facility offers several Scan^R screening microscopes,
data storage solutions and an image processing cluster.
- Scan^R microscopes features:
- MT20 ultra stable Xe light source (< 1% over 1000h)
- Scan^R real-time controller for precise and stable device control.
- Cell detecting autofocus (e.g focus only on metaphase cells)
- robotic gripper for microtiter plate handling
- 6x fluorescent channel + brightfield channel
Scan^R Publication
A microscope-based screening platform for large-scale functional protein analysis in intact cells
U. Liebel, V. Starkuviene, H. Erfle, J. Simpson, A. Poustka, S. Wiemann, R. Pepperkok - FEBS Letters, Volume 554, Issue 3, Pages 394-398
BLAST cluster board (Avi Epstein)
Status: 4000 search arrays/board. Features:
- 4000 search "CPUs" allow very fast genome/proteome sequence searches.
- Low power consumption compared to a "real cluster"
- No fans -> noise free
- Figure: Custom search engine board with up to 16 GByte memory (right)
- Bottom left: Four "ASIC CPUs" with 4x 1000 processor units each.
- Center: FPGA for data handling.
Current applications:
- The Bioinformatic Harvester allows text based searches.
The "Search-Cluster-Board" allows us to implement ultra fast sequence based searches.
Demo:
- Try it via Harvester --> Harvester sequence-search link
HWiKi - collaboration server and cool stuff
Hwiki is our collaboration server for (bioinformatic) projects. It offers
- Bioinformatic collaborations
- bioinformatic portals (e.g siRNA link collections)
- projects linking to bioinformatic harvester
- search engine portals
- student pages
- YaCy Sciencenet per start pages
- cool links :-)
Find the Hwiki here http://hwiki.fzk.de
