Preibisch Laboratory Follow @preibischs
Berlin Institute of Medical Systems Biology (BIMSB) of the
Max Delbrück Center (MDC)
Jobs availableFor my new lab at the Berlin Institute of Medical Systems Biology (BIMSB) I am looking for motivated PhD students and postdocs who are interested in working in the exciting interdisciplinary field of computational biology. We combine light & electron microscopy, transcription imaging and deep sequencing with computer vision and software development. We develop tools and solutions in order to study and model transcriptional regulation in development using C. elegans and other major model organisms.
For questions or more details on specific projects feel free to contact me. More details on specific projects can be found in the Open Positions page.
08/06/2015 4:57 pm
25/05/2015 2:13 pm
24/05/2015 4:45 pm
This image shows a downsampled subregion of one reconstructed & segmented slice of an electron microscopy (EM) acquisition covering an entire C. elegans in dauer stage, which we are using to build a computational model. The entire EM dataset was created during my time at HHMI Janelia (many thanks to Yalin Wang & Mei Sun from the EM facility for their amazing help) and consists of around 50.000 images distributed over 581 physical sections cut along the anterior-posterior axis of the nematode.
17/05/2015 5:22 pm
Images of Single-Molecule Fluorescent In-Situ Hybridization (smFISH) experiments in C. elegans showing the distribution of two (red, green) and one (gray) different species of single mRNA molecules throughout the entire specimen, nuclei are colored in blue.
17/05/2015 4:22 pm
My software for the reconstruction of multiview lightsheet microscopy now features a new interface alllowing for easy access to powerful reconstruction of lightsheet data. It is also fully integrated with the BigDataViewer for interactive browsing of terabyte sized datasets (publication accepted in Nature Methods). The code is open-source and is hosted on github.
17/05/2015 1:57 pm
We recently visited the new building site of the Berlin Institute of Medical Systems Biology (BIMSB) in the center of Berlin, it is happening.
13/11/2014 1:12 pm
13/11/2014 1:12 pm
Today I was stuck after my update to MacOS 10.10 to get Java3d running, getting the weird error:
04/09/2014 11:41 am
During the EMBO Practical Course on Lightsheet Microscopy my talk on multiview lighsheet registration was recorded.
This 30-minute talk covers the theory behind registration of multiview lightsheet microscopy data and it also quickly
addresses the problem of multiview fusion & deconvolution. A one-hour tutorial on the new
Multiview Reconstruction Plugin
is also available on YouTube.
09/06/2014 9:00 am
Figured out today that under the current version of Ubuntu (14.04) it is not advisable to use File>Connect to Server
to connect to a Samba server. I get dropped connections and just 50MB/s. When using:
23/05/2014 11:00 am
I used gource to visualize my implementations on the new
selective plane illumination microsopy
(SPIM) reconstruction branch. As always, the result looks great, I just stumbled over how to open the ppm-stream generated with:
19/05/2014 11:45 am
05/05/2014 1:10 pm
Today I installed Ubuntu 14.04 on my
Dell workstation, which has a
a Nvidia Quadro K4000 graphics card.
I therefore want to use CUDA and was planning to spend the rest of the day on the task of setting it up. To my suprise it was
ridiculously easy! The only slight problem was to actually get the CUDA
samples with it. Here is a short how-to:
25/04/2014 11:48 am
22/04/2014 3:32 pm
Our paper Efficient Bayesian-based multiview deconvolution finally got published in Nature Methods. Do not forget to check out the supplementary videos as well as the comprehensive supplementary methods document.
09/04/2014 12:32 pm
I arrived in Sydney and unfortunately Pavel Tomancak will not be able to join for the Focus on Microscopy. This increases this years' talk count to four:
09/02/2014 9:21 pm
02/02/2014 9:28 pm
Released my new software for multi-view dataset simulation, more details are available in the software section.
03/12/2013 11:00 am
Zeiss published a press release that comments on the 5th Annual LSFM Workshop in Thornwood, NY. Just noticed that I actually got mentioned personally in there.
11/11/2013 11:45 am
Today, I needed to connect to a samba share through an SSH-tunnel from my Mac. This does actually work pretty easily once you know how
(thanks to this blog). First you need to set up a loopback alias
as Mac refuses to connect to 127.0.0.1:
12/10/2013 11:44 am
I updated the Software section, it is up-to-date and contains the amazing "Game-of-Death" movie, an ImgLib2-based simulation, some details on ImgLib2, and a summary of all plugins for the reconstruction of Multi-View Light-Sheet Microscopy data.
12/10/2013 11:30 am
I just updated my Private section.
11/10/2013 7:26 pm
I updated the SPIM Multi-View Registration, Fusion and Deconvolution plugins to properly support the ImgLib CellContainer for opening files. This allows a seamless processing of SPIM input data files with more than 2^31 pixels (more than ~2048 x 2048 x 512px).
08/08/2013 7:19 pm
We submitted the new paper Efficient Bayesian Multi-View Deconvolution for Light Sheet Microscopy data a few weeks ago. The preprint is available on the
arXiv webpage. The software is as usual already available to everyone
as Fiji plugin, documentation can be found on the Fiji wiki.
10/06/2013 1:05 pm
I got awarded an HFSP Long-Term Fellowship which also implied switching to the lab of
Robert H. Singer at the Albert Einstein College of Medicine and HHMI Janelia Farm. The title of my project is:
10/06/2013 12:59 pm
The publishing business is not doing too bad recently. Our (Tobias Pietzsch, Stephan Saalfeld & me) beloved software project ImgLib2 finally got published in Bioinformatics. The paper accompanying our Fiji software was also recently published in Nature Methods. The paper of the OpenSPIM project is already available as advance online publication on the Nature Methods homepage, see publications section for more details.
20/01/2012 8:30 am
I released a new version of the Stitching plugin. It is available through Fiji and as a standalone download for ImageJ. You can now reconstruct arbitrarily sized, tiled acquisitions (which can be multi-channel, time-lapse stacks) with just very little RAM (even <1GB) if you activate the options to write the result directly to disk and/or open the input stacks only virtually! Here is a list of all new highlights:
24/10/2011 16:00 pm
I arrived in Janelia Farm where I am now in the group of Gene Myers. My new focus of research will be Caenorhabditis elegans.
03/04/2011 16:00 pm
27/12/2010 23:00 pm
Today, the renowned German newspaper Frankfurter Allgemeine Zeitung published an article on our latest publication in Nature. Another article in English was recently published by Deutsche Welle, an overview of the full press coverage can be found here.
27/10/2010 4:00 pm
The publishing business went very well the last couple of weeks as listed in the publication section.
I co-authored papers that analyze the co-transcriptional splicing with Fernando Carrillo-Österreich published in Molecular Cell,
the developmental hourglass with Alex Kalinka and Karolina Varga published in Nature, the electron microscopy analysis of the Drosophila brain
with Albert Cardona published in PLoS Biology, and the planar cell polarity signalling in zebrafish with Pablo Oteiza and Matthias Koeppen
published in Development.
14/06/2010 10:25 am
Pavel made it into the news today, a funny article about him and the stuff we are doing in his lab, written by Sabine Sütterlin: Wo Fruchtfliegenembryos zu Filmstars werden (German) (Where fruit flies become movie stars).
27/05/2010 5:10 pm
Our paper Software for bead-based registration of selective plane illumination microscopy data has been published today
by Nature Methods, check out the publication section.
20/04/2010 11:05 am
In the context of Fiji we (Stephan Saalfeld and me) released a first alpha version of ImgLib, a dimension-, storage- and data-type-independent image processing library for Java. If you want to try it please contact me!
20/04/2010 11:00 am
During the last month I was traveling a lot giving talks at the Focus on Microscopy Conference
in Shanghai as well as the 51st Annual Drosophila Research Conference in Washington and the
Janelia Farm Single Cell Biochemistry Consortium at the Janelia Farm Research Campus.
11/10/2009 5:40 pm
Three weeks ago I visited the very impressive International Symposium at the Studio Villa Bosch in Heidelberg, the topic was Subcellular Microscopy and Probing.
11/10/2009 11:52 am
We recently hosted The First Light Sheet based Fluorescence Microscopy Workshop here in the MPI in Dresden. The workshop turned out to be very interesting and helpful, the aims are now to start building a light sheet community via the conference webpage.
11/10/2009 11:50 am
This summer I have been to the 17th International C. elegans Meeting in Los Angeles where I presented our Bead-based registration
framework and it's applicability to high-resolution C. elegans imaging.
05/04/2009 1:01 pm
I have been attending the Focus on Microscopy conference in Krakow, Poland. The conference was really good, I will try to go next year to Shanghai again. A link to the abstract my presentation can be found here.
03/02/2009 1:16 pm
I am soon leaving for the SPIE Medical Imaging Conference in Orlando/Florida presenting our newest paper.
02/02/2009 9:16 pm
I had serious issues solving a memory problem under MikTeX (Win32) using pdflatex (TeX capacity exceeded, sorry [main memory size=1500000]). Altough changing the configuration files as proposed in the manual (initexmf --edit-config-file=pdflatex) the max memory only increased to 3.6MB. There are also thousands (not that many but it feels like that) command line options which are supposed to solve the problem, however only one of them worked, which is --extra-mem-top=n. I hope this can help somebody who is stuck with the same problem.
08/12/2008 10:16 pm
I am currently visiting Albert Cardona's lab at the INI Zürich for another Hackathon. I hope to get a lot of stuff done I usually do not work on.
17/09/2008 11:21 am
17/09/2008 11:20 am
In November the annual ImageJ conference will take place in Luxembourg, I will give a presentation as well.
06/08/2008 9:50 pm
Our two papers describing the Hook Method in detail have been accepted today. I will put them for download the publications section as far as the last changes have been made.
31/07/2008 9:09 pm
A lot of stuff happened in the last half of the year. I went to the Focus on Microscopy Conference
in Osaka/Japan and the IEEE ISBI in Paris/France to present my new SPIM
registration algorithm (details here). We also had another amazing hacking event
at the Janelia Farm Research Campus near Washington D.C.
17/02/2008 7:09 pm
You can finally download the first offical release of the Hook-Method for Microarray Data Analysis in the Software Section. You will also find the corresponding paper there. I also presented the Hook-Method at the Terry Speed Group Meeting on the 25/01/2008 in Berkeley.
30/12/2007 7:33 pm
target="_blank"Dr. Hans Binder presented our work
on the analysis of Microarray Data at the BioInfo Summer 2007
in Canberra, Australia.
30/12/2007 7:33 pm
I am visiting the SPIE Medical Imaging Conference which takes place in San Diego from the 16th till the 21st February. I'll give a talk on Mosaicing of Single Plane Illumination Microscopy. Before that I'll stay for 5 weeks at the Stanford Research Institute in the lab of Torsten Rohlfing.
12/10/2007 2:01 pm
I am impressed how easy it was to install Ubuntu 7.10 x64 edition on the M1330. There were just no problems and everything worked immediately. Unfortunately it seems it is not possible to attach another monitor with a different resolution than the LCD screen of the notebook. I hope this issue will be fixed with one of the next updates.
12/06/2007 4:36 pm
I finally got my new notebook, it is a nice Dell M1330. I like it so far, especially the LED screen
is just amazing. Nevertheless I had some problems installing WindowsXP x64 as Dell does not provide
all drivers for the 64 Bit operating systems. For all those out there who have the same problem i
wrote a small HowTo, see here:
Dell M1330 WindowsXP x64 Installation HowTo
11/07/2007 1:51 pm
We got an article in the HHMI (Howard Hughes Medical Institute) Bulletin about the great Hackathon at Janelia Farm this summer. Thanks again to Albert Cardona and Arnim Jenett for organizing this event and Gerald M. Rubin for the sponsoring!
11/07/2007 1:30 pm
Dr. Hans Binder from the IZBI
we finally finished the first publication on our Oligo-Method for analyzing gene expression arrays.
11/07/2007 1:28 pm
I am really happy that I got accepted together with Torsten Rohlfing for the SPIE Medical Imaging Conference in San Diego in February. I'll also spend some time before at his institute (Stanford Research Institute) in San Fransisco.
11/07/2007 1:01 pm
Lots of stuff happened since my last entry. I held my first talk at a big conference in Vienna, the EDRC 2007 which was a great event.
20/08/2007 3:18 pm
My next TAC meeting is on 19th September. Learn more ....
20/08/2007 3:18 pm
I am visiting CAIP 2007 in Vienna from 26th August till 30th August. Learn more ....