User Tools

Site Tools


Sidebar

Top
Seminar
Courses
Textbooks
Documents
Downloads
Weblog
RSS aggregates
Discussions
Archives


EMBL BioImage Data Analysis

EuBIAS

NEUBIAS

—- Contact
CMCI Alumni
ALMF
EMBL Heidelberg
EMBL Intranet


Popularity Ranking


Timeline of @cmci_

cmci_ avatar

strong recommendation to take a look at this: #NEUBIAS volks! "The Practice of Reproducible Research" https://t.co/ISqh2kysos
About 5 days, 3 hours ago by: Kota Miura (@cmci_)

cmci_ avatar

@pablo_jack yes, combining morphology operations
About 1 week ago by: Kota Miura (@cmci_)

cmci_ avatar

@pablo_jack pls try, and your comment is welcome to polish the text.
About 1 week ago by: Kota Miura (@cmci_)

cmci_ avatar

@pablo_jack the method explained in the draft is widely used method for segmenting rim of a structure.
About 1 week ago by: Kota Miura (@cmci_)

cmci_ avatar

@pablo_jack here is a draft of a chapter for the future 2nd edition of our textbook: https://t.co/3FXnPtX1NC nuclear rim segmentation
About 1 week ago by: Kota Miura (@cmci_)

cmci_ avatar

@pablo_jack Quimp would be an overkill...
About 1 week ago by: Kota Miura (@cmci_)
downloads:start

Downloads

Bioimage analysis tools developed by Kota and offered for free download are listed here. 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
Course Course Utilities ImageJ Kota MIura 2016-04-22
Visualization 3D track viewer ImageJ Kota Miura 13-11-27
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 12-11-24

Un-Documented Codes

Some of the codes, still not documented.

Scripts

  • ijmacros/dataconvert/MTrackJ23Dviewer.py at master · cmci/ijmacros · GitHub (2012/07/11 05:36)
    Jython script for converting MTrackJ output file to a data format readable by 3D track viewer plugin.  Tags: ijmacro jython coding
  • kymotrackPlotter.py (2012/04/25 07:07)
    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 07:05)
    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 dynamicsnote: 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 04:58)
    reuires: Bleach Correction plugin (or Fiji) Does bleach correction using Histogram matching method in headless environment. e.g. fiji -headless bleachCorHM.js Tags: imagej fiji headless bleachCorrection
  • Correct_3D_drift_headless.py (2012/04/25 04:49)
    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 04:44)
    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). Tags: ImageJ 3Dplotter 4Dstack ParticleTracker3D
  • zprojSUM_LIF_headless.py (2012/04/25 04:43)
    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 04:41)
    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 04:40)
    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 04:14)
    Loads csv files with feature points and transforms 3D stack. Tags: fiji 3Dregistration affinetransform javascript
  • K_3Dprofile.js (2012/04/25 04:13)
    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. Tags: ImageJ 3Dmeasurement fiji IntensityProfile javascript
  • 3DdiscV3.js (2012/04/25 04:13)
    Requires: Fiji 3D disc generator using commons Vector3D A part of 3D intensity profiler. Tags: ImageJ fiji IntensityProfile 3Dmeasurement javascript
  • Dot3Danalysis.py (2012/04/25 04:10)
    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. Tags: jython myscripts 3ddots ImageJ 3dtracker
  • 3Ddots.js (2012/01/26 03:23)
    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). Tags: ImageJ 3Dplotter 4Dstack ParticleTracker3D
  • K_LIFfileImporter.ijm (2012/01/26 02:56)
    ImageJ macro for opening specific channel in LIF dataset. Tags: ImageJ fileIO ImageJmacro
  • highpassFilter.py (2012/01/26 02:47)
    High-pass filter using scipy and numpy.  Tags: python26 scipy numpy filter
  • batchXls2csv.py (2012/01/26 02:45)
    Batch conversion of excel file to csv file Tags: python26 utilities excel csv
  • loadVecandMayaviPlot.py (2012/01/26 02:43)
    Loads vectors (csv file) and plots as a 3D vector field in mayavi Tags: python26 mayavi 3Dvisualization vectorfield
  • openTiffAsVolume.py (2012/01/26 02:41)
    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

  • DotLinker (2012/02/20 06:04)
    Linking algorithms for tracking. Segmentation should be done in separate process.  Tags: imagej plugin tracking
  • RadialProfileV2 (2012/02/20 06:02)
    Bug fixed version of Radial Profile Plugin in ImageJ website. Tags: imagej plugin measurements
  • CourseModules (2012/02/20 06:01)
    A collection of plugins for teaching Tags: imagej plugin courses
  • emblTools (2012/01/26 02:18)
    Requires: ImageJ Misc. utilities for image processing. 4D stack extraction from 4D stack For a specific case: 3D stack extraction from 4D stack Silent (no dialog) FFT filtering for use in cluster Tags: myplugins ImageJ 4Dstack utilities

Notes

downloads/start.txt · Last modified: 2016/05/31 06:26 by kota