Plots Bory project tracking results onto 3D-kymograph.
noteFilepath and dimension of the kymograph should be adjusted manually.
Tags:
imagej
fiji
projection
jython
kymograph
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
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
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).
Tags:
ImageJ
3Dplotter
4Dstack
ParticleTracker3D
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
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
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
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.
Tags:
ImageJ
3Dmeasurement
fiji
IntensityProfile
javascript
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.
Tags:
jython
myscripts
3ddots
ImageJ
3dtracker
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).
Tags:
ImageJ
3Dplotter
4Dstack
ParticleTracker3D
Requires: Python (wrote with 2.6)
+ additional modules Mayavi, tiffile, tkFileDialog
Loads a tiff stack and display it in mayavi.
Tags:
python26
mayavi
3Dvisualization