JFilament is an ImageJ plugin for segmentation and tracking of 2D filaments in fluorescenece microscopy images. The main algorithm used in Jfilament is "Stretching Open Active Contours".
This site has the source code of the project. For a compiled version and for user instructions go to https://www.lehigh.edu/~div206/jfilament/ .
This work is supported by NIH and by the Biosystems Dynamics Summer Institute at Lehigh University.
Version 1.2.0
- Removed JFilament3D
- Added plugin for labelling image
- Added option to deform all of the snakes in every frame. Version 1.1.9
- Added deform all by holding ctrl and clicking.
- Deprecating JFilament3D. I don't think it is getting used, and it add some dependencie wieght.
Version 1.1.8
- SnakeSculpting now has a dialog for adjusting the size by holding ctrl + clicking.
- Zoomed in view is now draggable.
- Balloon intensity energy is now the stretch force for closed contours foreground/background values.
- More labelling options. Can label an image with the id of the snake as the color.
- Snake Id's can be displayed on the main screen by pressing
i - Produce 'labelled image' with regions filled per contour.
- Produce distance transform.
- Updates to 3D viewer.
Version 1.1.7
- Clear current snake.
- Create a mask image using snakes.
- Look at function for 3D viewing.
- BUG FIX: removing snake by deleting all of its points sometimes caused a crash.
Version 1.1.6
- BUG FIX: A class file was omitted from mvn package.
- Introduced a new 2D plugin for kimographs.
Version 1.1.5
- Improved view rotation and controls.
Version 1.1.4
- sculpting of snakes. By pressing 's' when a snake is selected, the snakes can be sculpted, points moved around.
- contrast. The display range of the image can be changed.
- indicator in the corner now indicates which snake is being modified, should correspond with snakes saved in file.
- Building/Versioning update.
References:
M. B. Smith, H. Li, T. Shen, X. Huang, E. Yusuf, and D. Vavylonis, "Segmentation and Tracking of Cytoskeletal Filaments using Open Active Contours," Cytoskeleton 67:693-705 (2010)
H. Li, T. Shen, M. B. Smith, I. Fujiwara, D. Vavylonis, and X. Huang, "Automated Actin Filament Segmentation, Tracking, and Tip Elongation Measurements based on Open Active Contour Models," In Proc. of the IEEE International Symposium on Biomedical Imaging: From Nano to Macro, ISBI-09, Boston, 2009