Contact

Max Planck Institute of Molecular Cell Biology and Genetics
Pfotenhauerstr. 108
01307 Dresden, Germany

phone +49 351 210-2753
fax+49 351 210-1389

saalfeld@mpi-cbg.de

News Archive

Tue, 15 Mar 2011: Elastic Alignment and Montage for Fiji
We made available an impementation of a long standing idea for elastic series alignment and montaging dating back to a poster presented in 2008. The project has been on hiatus for long time since other projects have been more urgent. Recently, it has been resurrected for some data that actually needs it.
Thu, 10 Feb 2011: Back from Madison, Fiji Hackathon
I met many interesting and dedicated people and, together with Tobias Pietzsch and Stephan Preibisch, got a lot of work done on ImgLib2. Many thanks to our hosts, Kevin Eliceiri and Curtis Rueden at LOCI.
Wed, 1 Sep 2010: CLAHE plugin for Fiji/ImageJ updated
We added support for multi-channel images (in ImageJ, this is entirely different from RGB…). That is, the plugin is now ready to be used for local contrast compression of HDR images with 16-bit or 32-bit color channels.
Mon, 30 Aug 2010: Back from a short trip to Zürich, visiting Albert Cardona
Albert hosted a small meeting together with Stephan Gerhard and Mark Longair with a focus on coding CATMAID. The project is in a state of flux again…
Thu, 12 Aug 2010: CLAHE plugin for Fiji/ImageJ updated
We implemented the faster version of CLAHE as described in the literature. Instead of evaluating the intensity transfer function for each pixel independently, only a grid of adjacent boxes is evaluated and locations in between interpolated.
Tue, 3 Aug 2010: Simple Panorama Viewer for Fiji/ImageJ
Playing around with coordinate spaces, we built a simple interactive panorama viewer for ImageJ/Fiji. Check it out and have fun.
Thu, 15 Jul 2010: Back from Boston, ISMB 2010
I was talking about ssTEM registration and visited Davi Bock and Ignacio Arganda-Carreras.
Fri, 12 Mar 2010: Fiji mpicbg-package updated
Feature Extraction considers the user-defined visible contrast range. Thanks to Ignacio Arganda-Carreras and Kannan U. V. for pointing out that the previous behavior had its shortcomings.
Fri, 5 Mar 2010: Back from VizBi at EMBL
Pavel Tomančák talked about microscopy and registration and I presented a poster about TrakEM2 and CATMAID.
Fri, 19 Feb 2010: Finished registration of Albert Cardona's fantastic ssTEM data set
The data set shows an abdominal segment of the VNC of a Drosophila first instar larva, that is a volume of 80×50×23μm in 459 serial sections of 50nm, overall 33,499 non-empty images at 4nm/px. Watch this movie to get an idea. While running this, I fixed several tiny bugs that were slowing down the process.
Sat, 30 Jan 2010: Visited Albert Cardona at INI for coding TrakEM2
The alignment of multi-layer mosaics can now calculate a smooth continuous deformation for each layer instead of just rotating and shifting the tiles. The amount of layer-deformation is adjustable through the weights of intra-layer vs. cross-layer point matches.
Wed, 16 Dec 2009: New personal website
Have fun with my new website.
Thu, 26 Nov 2009: CLAHE plugin for Fiji/ImageJ
Added mask support to the CLAHE plugin. The dialog offers all images with the same dimensions as the current image as possible masks. Combining Rois and masks is possible and a powerful tool.
Sat, 14 Nov 2009: CLAHE plugin for Fiji/ImageJ
Inspired by the work of Pavel Koshevoy, we implemented the Contrast Limited Adaptive Histogram Equalization (CLAHE) as an ImageJ plugin and put it into Fiji. A manual page is available at the Fiji-Wiki.