TrakEM2
What is it?
TrakEM2 is an ImageJ plugin for morphological data mining, three-dimensional modeling and image stitching, registration, editing and annotation.Snapshots
Four movies:
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See a lot more snapshots and movies.
TrakEM2 video tutorials for users.
Latest news
Download latest Fiji with TrakEM2 or go to menu "Help - Update Fiji".Pull source code from the git repos.
Stay up to date with Fiji.
TrakEM2 class diagram for programmers.
TrakEM2 video tutorials for users.
2009-10-01 - 0.7l released
- Improved semiautomatic segmentation by fast-marching: there is a bounding box now that limits maximum growth, which is resizeable by shift+scrollwheel. The read out of the grown mask is faster, by scanning lines.
- Added lasso tool by Johannes Schindelin as part of the PENCIL semiautomatic segmentation of an AreaList. control+drag will run the lasso tool on a selected AreaList.
- Added layer composites on LayerPanel right-click menu. Some fixes to repainting on "Reset all layer [colors|alphas|composites]"
- Fixed error in filling alpha masks with 'f' using current ROI over selected image patches. This fix works around an error in java.awt.geom.Area.intersect(Area(Rectangle)) and in ij.gui.ShapeRoi.getMask().
- Fixes in exporting arealists as labels: only up to 255 for 8-bit (not 256; 0 is background) and proper cropping of the ShapeRoi to work around the ImageProcessor.fill(ShapeRoi.getMask()) error in ImageJ.
- Preventing AreaList from painting beyond srcRect, in a nice unobtrusive way.
- Fixed error in creating undo steps for renaming nodes in the trees and for adding new nodes or moving or removing them.
- Lens distortion model visualization now takes far less memory resources, thanks to Stephan Saalfeld.
- Reworked lock/unlock logic; now the flag is updated on the spot for all linked displayables. Otherwise, it doesn't scale at all.
- Improvemenets in the Display GUI logic.
- Fixed creation of subprojects; was broken since the introduction of the UNUId system. Also fixed the opening of a properly scaled canvas in the display for the new subproject.
- Better reporting on what the undo/redo command did, in the log window.
- Better repainting of AreaList after brushing.
2009-09-18 - 0.7k released
- Added new Stack data type, useful for overlaying confocal image stacks on serial section electron microscopy images. Setup landmarks (a node with only "ball" children, where each ball has a single x,y,z point) for both a project with a confocal stack and a project with serial section TEM, and use "Import - Import stack with landmarks". Useful as well for importing from confocal to confocal (by Stephan Saalfeld).
- Added new color composite mode, which is a property of each Displayable object (an image, a pipe, an arealist, ...). Select one, right-click and select "Properties..." and choose among normal, add, subtract, multiply, difference and color (YCbCr) (by Stephan Saalfeld).
- Added a deform option to the multi-layer mosaic image registration (by Stephan Saalfeld).
- Fixed a number of file path-related bugs for MS Windows.
- Fixed creation of subprojects. Now arealists, pipes, ball, etc., are cropped to the desired layer range.
- More robust memory management.
- Greatly improved speed of putting objects in the 3D Viewer.
- Improved mipmap regeneration queueing.
- Numerous small fixes and improvements.
Thanks to Stephan Saalfeld for developing numerous features and bug reports, and German Koestinger for bug reports and testing.
2009-08-27 - 0.7j released
- Improved lens distortion correction thanks to Stephan Saalfeld. See this and this.
- Added paint modes to AreaList: allow overlap, exclude others and erode others. Choose the radiobutton under the tools in the Display when using the PEN tool to brush in an AreaList.
- Stephan Saalfeld fixed bug 71.
- Not showing annoying import stack dialog when it's clear which stack is to be imported. After suggestion/reminder from Christian Niedworok.
- Added a reverse command to Pipe. Pipe also paints a number '1' next to the first point, to disambiguate pipe direction.
- Added surface (lower and upper bound estimates) and maximum diameter measurements to AreaList, after request from Javier Cabrera Chaves. See arealist measurements for all details.
Read all news here.
Download and Install
Managed installation:- Download latest Fiji with TrakEM2 or go to menu "Help - Update Fiji".
- Stay up to date with Fiji.
- Compile from source -- has lots of .jar file dependencies.
- Requires ImageJ ij143a or above.
What can you do with it?
- Semantic segmentation editor: order segmentations in tree hierarchies, whose template is exportable for reuse in other, comparable projects.
- Model, visualize and export 3D.
- Work from your laptop on your huge, remote image storage.
- Work with an endless number of images, limited only by the hard drive capacity. Dozens of formats supported thanks to ImageJ.
- Import stacks and even entire grids (montages) of images, automatically stitch them together and homogenize their histograms for best montaging quality.
- Add layers conveniently. Each layer has its own Z coordinate and thickness, and contains images, labels, profiles...
- Insert layer sets into layers: so your electron microscopy serial sections can live inside your optical microscopy sections.
- Run any ImageJ plugin on any image.
- Measure everything: areas, volumes, pixel intensities, etc. using both built-in data structures and segmentation types, and standard ImageJ ROIs. And with double dissectors!
- Visualize RGB color channels changing the opacity of each on the fly, non-destructively.
- Annotate images non-destructively with floating text labels, which you can rotate/scale on the fly and display in any color.
- Montage/register/stitch/blend images manually with transparencies, semiautomatically, or fully automatically within and across sections, with translation, rigid, similarity and affine models with automatically extracted SIFT features.
- Correct any lens distortion present in the images, like those generated in transmission electron microscopy.
- Add alpha masks to images using ROIs.
- Undo all steps.
How does it work?
TrakEM2 has been written in Java as an ImageJ plugin, and contains a virtualization engine for seamlessly working with arbitrarily large datasets, limited only by your file storage capacity.Two independent modalities exist: either XML-based projects, working directly with the file system, or database-based projects, working on top of a local or remote PostgreSQL database.
Authors
TrakEM2 is the design child of Rodney Douglas and Albert Cardona, with the help of the entire Institute of Neuroinformatics, University of Zurich / ETH, and has been implemented by Albert Cardona.Stephan Saalfeld and Stephan Preibisch, from Pavel Tomančák's group, have written the libraries responsible for phase-correlation, cross-correlation, scale invariant feature transform, and associated utilities such as proper, gaussian-exact image resizing and automatically multithreaded processing routines that adapt to the machine's available cores.
Acknowledgements
TrakEM2 would not have been possible without the continuous help from ImageJ's author, Wayne Rasband, and the economic support to Albert Cardona from both Rodney Douglas at INI and Volker Hartenstein (NIH Grant NS054814) at the University of California Los Angeles.We are also particularly grateful to David Lawrence for his assistance in PostgreSQL, and also to Nuno da Costa, Rita Bopp, Lauriston Kellaway, John Anderson, Wayne Pereanu and Davi Bock for their input.
3D visualization and mesh-making by marching cubes have been possible thanks to Bene Schmid and Johannes Schindelin from Würzburg.
Image stitching has been made possible thanks to Stephan Preibisch, and the web viewer thanks to Stephan Saalfeld, both from Pavel Tomančák's in the Max Plank Institute for Cell Biology and Genetics, Dresden.