Downloads
We welcome your comments and suggestions.
| Type | Name | Platform | Author | Last UpDate |
|---|---|---|---|---|
| Analysis | Frap Analysis ver 9 | IgorPro | Kota Miura | 10-03-03 |
| Spindle FRAP/FLIP analyze | ImageJ | Kota Miura | 08-08-12 | |
| Kymoquant | ImageJ | Kota Miura | 10-03-03 | |
| – automated analysis of kymograph | ||||
| ParticleTracker | ImageJ | Kota Miura | 10-11-19 | |
| Stack Tools | Time Series color coder | ImageJ | Kota Miura | 08-07-23 |
| Running 3D-Projector | ImageJ | Kota Miura | 08-08-29 | |
| Stack Manager | ImageJ | Kota Miura | 06-06-08 | |
| Bleach Corrector | ImageJ | Kota Miura | 12-04-23 | |
| Visualization | 3D track viewer | ImageJ | Kota Miura | 12-04-23 |
| File Conversion | Perkin Elmer Tiff Series to 3D stacks for 3D Manual Tracking | ImageJ | Kota Miura | 07-06-05 |
| DeltaVision Format Header Reader for Collapsed .dv files | ImageJ | Kota Miura | 07-06-13 | |
| Software Linker | Export Hyperstack to Imaris | ImageJ/Imaris | Kota Miura | 10-08-06 |
| Coding Tools | Notepad++ Syntax High-Lighter for ImageJ Macro | Notepad++ | Kota Miura | 10-11-00 |
| Vim Syntax High-Lighter for ImageJ Macro | VIM | Kota Miura | 10-11-29 | |
| Drop Script | ImageJ | Kota Miura | 12-02-19 |
Un-Documented Codes
Some of the codes, still not documented.
Scripts
- kymotrackPlotter.py (2012/04/25 16:07)
Plots Bory project tracking results onto 3D-kymograph.
noteFilepath and dimension of the kymograph should be adjusted manually.Tags: imagej fiji projection jython kymograph
- 3dprojection.py (2012/04/25 16:05)
4D stack kymograph (by maximum projection)
requires a 3D timeseries (4D hyperstack) to be opened.
Outputs three 2D kymographs (xz, yz, xy projections to y, x, z axes, respectively)
...written in conjunction with Bory's project on chromosome locus distance dynamics
note: z is not scaled by XY scale, so the width of xy projection image
# should be adjusted by resizing according to z factor.Tags: imagej fiji projection jython kymograph
- bleachCorHM.js (2012/04/25 13:58)
reuires: Bleach Correction plugin (or Fiji)
Does bleach correction using Histogram matching method in headless environment.
e.g.
fiji -headless bleachCorHM.jsTags: imagej fiji headless bleachCorrection
- Correct_3D_drift_headless.py (2012/04/25 13:49)
Requires: Fiji
Headless version of Correct 3D drift written by Robert Bryson-Richardson and Albert Cardona. For use from command line, such as
./fiji Correct_3D_drift_headless.py file_path destination_folder
arg1 is the full path to the file to be corrected, and the destination folder is where the corrected stack is saved.Tags: imagej fiji 3Dregistration headless
- 3Ddots.js (2012/04/25 13:44)
script for 3D spot detection using ParticleTracker3D and creating a stack with same size of the current stack, and plot xyz dots listed in results window (the results of ParticleTracker3D plugin).
- zprojSUM_LIF_headless.py (2012/04/25 13:43)
Z-sum-projection script for LIF file.
works from command line, intended to be used in server - data storage.
Useful for processing huge data sets without occupying your desktop.Tags: ImageJ 4Dstack Cluster headless projection
- zproj_TifSeries_headless.py (2012/04/25 13:41)
Z-max-projection script for Tiff series.
works from command line, intended to be used in server - data storage.
Useful for processing huge data sets without occupying your desktop.Tags: ImageJ 4Dstack Cluster headless projection
- zproj_LIF_headless.py (2012/04/25 13:40)
Z-max-projection script for LIF file.
works from command line, intended to be used in server - data storage.
Useful for processing huge data sets without occupying your desktop. For converting stacks within .lif file to z-projected tiff stacks in file server. All files within the directory given as the first argument will be processed.
e.g.
fiji headlessZprojector.py /g/cmci/test/Tags: ImageJ 4Dstack Cluster headless projection
- affinetransform3Dv3.js (2012/04/25 13:14)
Loads csv files with feature points and transforms 3D stack.
- K_3Dprofile.js (2012/04/25 13:13)
Requires: Fiji
...or ImageJ with Apache commons math.
3D intensity profiler, from a list of coordinates (start point and end point) in csv file.
workflow: prepare a tab-delimited data file with a pair of 3D coordinates per line(6 numbers per line).
Run this script, and in dialog window choose the file, then 3D intensity profile in the top-image window will be calculated and shown in the Results table. - 3DdiscV3.js (2012/04/25 13:13)
Requires: Fiji
3D disc generator using commons Vector3D A part of 3D intensity profiler. - Dot3Danalysis.py (2012/04/25 13:10)
Requires: ImageJ, DotDetector3D plugin (ask Kota).
Dot detection by segmentation of ch1 and measures ch2 with a bit wider area.
Dot coordinates are detected in 3D. Multiple dots being too close to each other are omitted from measurement since with the application this code was written, focal depth is thick. 3D intensity measurement is currently omitted. - 3Ddots.js (2012/01/26 12:23)
script for 3D spot detection using ParticleTracker3D and creating a stack with same size of the current stack, and plot xyz dots listed in results window (the results of ParticleTracker3D plugin).
- K_LIFfileImporter.ijm (2012/01/26 11:56)
ImageJ macro
for opening specific channel in LIF dataset.Tags: ImageJ fileIO ImageJmacro
- highpassFilter.py (2012/01/26 11:47)
- batchXls2csv.py (2012/01/26 11:45)
- loadVecandMayaviPlot.py (2012/01/26 11:43)
Loads vectors (csv file) and plots as a 3D vector field in mayavi
- openTiffAsVolume.py (2012/01/26 11:41)
Requires: Python (wrote with 2.6)
+ additional modules Mayavi, tiffile, tkFileDialog
Loads a tiff stack and display it in mayavi.Tags: python26 mayavi 3Dvisualization
Plugins
- RadialProfileV2 (2012/02/20 15:02)
Bug fixed version of Radial Profile Plugin in ImageJ website.
Tags: imagej plugin measurements
- CourseModules (2012/02/20 15:01)
Notes
see also download page in ALMF site.
Export to OpenOffice- Tools:
Discussion