Homepage of Stephan Preibisch                     

HFSP Fellow in the labs of Robert H. Singer and Eugene Myers at the Albert Einstein College and the MPI-CBG
Visiting Scientist at the HHMI Janelia Farm Research Campus

News

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:

sudo mount -t cifs //sambaserver/directory /local/mount/path -o username=name

instead everything works great, and that with 100MB/s.

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:

  • gource -800x600 SPIM_Registration/ -stop-at-end -s 0.25 -highlight-all-users -start-position 0.76 -o animation.ppm
using Fiji. At the end, it is pretty easy, you simply have to:
  • File > Import > RAW
  • Image type: 24-bit RGB
  • Width: 800
  • Height: 600
  • Offset to first image: 37
  • Number of image: filesize[bytes] / (800*600*3+37)
  • Gap between images: 37
Alternatively, one can directly export it as H.264/MPEG-4, in case one manages to install ffmpeg on Ubuntu 14.04, here is a how to. Make sure to follow the first answer in order to install it using the package manager. Then, you can for example call directly:
  • gource -800x600 SPIM_Registration/ -stop-at-end -s 0.25 -highlight-all-users -start-position 0.76 --output-ppm-stream - | ffmpeg -f image2pipe -vcodec ppm -i - -y -vcodec libx264 -b 3000k -maxrate 15000k -r 50 visualization.mp4

  • and the final result is:


19/05/2014 11:45 am

Our multiview deconvolution paper got an article on the HFSP website today, check out our videos as well:

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:

Install the CUDA toolkit (only gives you version 5.5, but that's fine for me)
sudo apt-get install nvidia-cuda-toolkit

Download the samples (RUN format for Ubuntu 12.04) from the NVIDIA website
https://developer.nvidia.com/cuda-toolkit-55-archive

Extract only the samples (adjust directory accordingly)
./cuda_5.5.22_linux_64.run -extract=/home/preibisch/Downloads

Install the samples
./cuda-samples-linux-5.5.22-16488124.run
The path for nvcc is: /usr/lib/nvidia-cuda-toolkit/
I installed it in /home/preibisch/cuda-samples (no sudo required)


Here are some more libraries you will need to compile all examples
sudo apt-get install libglu-dev freeglut3 freeglut3-dev libxmu-dev libxi-dev mpi-default-dev

Now you can build all the samples
cd ~/cuda-samples
make

25/04/2014 11:48 am

The MPI-CBG released a news entry describing our new paper Efficient Bayesian-based multiview deconvolution. The article is also available in German.

NM Homepage on April 22nd 2014

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.

NM Homepage on April 22nd 2014 Screenshot of the Nature Methods homepage retrieved on April 22nd 2014.

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:

  • Open-source software for the reconstruction and analysis of light-sheet microscopy data
    (Sun, Apr 13, 14:00 - 16:45, Reginald Theater, Tutorial)
  • Reconstruction of multi-focal microscopy data
    (Mon, Apr 14, 14:00 - 14:20, Reginald Theater, Presentation)
  • OpenSPIM - An open access platform for selective plane illumination microscopy
    (Tue, Apr 15, 12:20 - 12:40, Studio 1, Presentation)
  • Efficient bayesian-based multi-view deconvolution
    (Tue, Apr 15, 14:00 - 14:20, Everest Theater, Presentation)

09/02/2014 9:21 pm

I got accepted for a tutorial and two talks at this years' Focus on Microscopy in Sydney, Australia. Looking forward to a great conference, more details are in the Conferences and Events section.

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:

sudo ifconfig lo0 127.0.0.2 alias up

Now you set up your SSH-tunnel that forwards the ports 139 and 445:

sudo ssh -L 127.0.0.2:139:samba-server:139 -L 127.0.0.2:445:samba-server:445 user@ssh-login-server

In case that the samba-server and the ssh-server are the same machine simply replace samba-server with localhost. Now, you can connect to the server:

Go -> Connect to Server ... -> smb://sambauser@127.0.0.2/

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.
Note that this software can process data acquired by the new Zeiss Lightsheet Z.1 microscope. Prerequiste is currently to save each view as an individual CZI file.

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:
In-toto analysis of the signaling network regulating C. elegans dauer diapause
More details can found on the HFSP website (LTF, 2012).

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:

  • supports composite images and hyperstacks now (arbitrary amount of channels and time-points)
  • can optionally write the stitched image slice-by-slice directly to disk (significantly reduces the RAM requirements)
  • can optionally open the input images as Virtual Stacks (significantly reduces the RAM requirements)
  • supports timelapse alignment with different stitching options
  • subpixel-resolution
  • supports many different types of grids (row-by-row, column-by-column, snake, ...)
  • can read the approximate tile positions from the image metadata
  • finally based on ImgLib
There are only two plugins left, they replace the Stitching2D/3D and the Stitch Grid, ... Sequence, ... Collection and so on. They are called:
  • Stitching -> Pairwise Stitching
  • Stitching -> Grid/Collection Stitching
You can find a complete documentation on the Fiji-wiki. I thank all the authors of the necessary libraries and other people who helped me with the stitching.

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

The list of the 2011 finalists for the Drosophila Image Award has been published. Our movie picturing Drosophila development in its entirety is one of the candidates, it is also available on YouTube.

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.
Together with Stephan Saalfeld we also published in the conference proccedings of the ImageJ Conference 2010 describing our Java image processing framework ImgLib.

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.
The corresponding software will be released next week with the new Fiji "Heidelberg" Release!

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.

Furthermore, I participated in a new Hackathon which was held at the EMBL in Heidelberg. During the meeting we organized a workshop on Image registration together with Stephan Saalfeld and Ignacio Arganda. Thanks a lot to Kota Miura and Francesca Peri from the EMBL for hosting us.

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.
On the way back I stopped in the lab of Rob Singer at the Einstein College in New York to present our work as well, it was a very nice experience.

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

The provisional PDFs of our Hook calibration papers are now available for download from the Algorithms for Molecular Biology Website. You can find the direct links in the publications section.

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.
Soon I will officially release the new Stitching Package for ImageJ, it is now possible to stitch complete 3D grids of images, globally optimized (thanks to Stephan Saalfeld) and nicely intensity adjusted. I will present it on the ImageJ conference in November, a preliminary package is available here. It contains as well the Stiching2D and Stitching3D plugins for stitching two images.

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.
The Oligo-Software will hopefully be released next week. You will be able to download it in the Software Section and on the IZBI Homepage.

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

Tomorrow I will install Ubuntu 7.10, let's see how this goes. :)

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

Together with Dr. Hans Binder from the IZBI we finally finished the first publication on our Oligo-Method for analyzing gene expression arrays.
The Java program will be published in my Software section.

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 ....