User Tools

Site Tools


Sidebar

Top
Profile
Seminar
Courses -2016
Courses 2018-
Textbooks
Documents
Downloads (-2016)
Downloads (2016-)
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

RT @_pm_lab: Unbiased quantitative phenotypic #BioImageAnalysis of #3D #microscopy images in #HighContentScreening is a fundamental challen…
About 6 hours, 43 mins ago by: Kota Miura (@cmci_)

cmci_ avatar

RT @joachimgoedhart: Our recent preprint has several step-by-step guides that explain how timelapse imaging data can be processed and visua…
About 5 days, 6 hours ago by: Kota Miura (@cmci_)

cmci_ avatar

RT @PLOSCompBiol: 3D #BioImageAnalysis for #HighContentScreening should be easy. Using data driven voxel-based features & #MachineLearning…
About 6 days, 22 hours ago by: Kota Miura (@cmci_)

cmci_ avatar

RT @ArizonaImaging: ImageJ/FIJI ASU TEC Talk, Thursday March 18. Learn about techniques at the beginner and advanced in a two-part workshop…
About 6 days, 22 hours ago by: Kota Miura (@cmci_)

cmci_ avatar

RT @jan_eglinger: Batch processing, image and data analysis with visual workflows using #KNIME - join @stelfrich and myself this Thursday f…
About 1 week ago by: Kota Miura (@cmci_)

cmci_ avatar

RT @DrAnneCarpenter: Postdoc opening in Boston! Your expertise in machine learning, statistics and/or data science can be splendidly appli…
About 1 week, 2 days ago by: Kota Miura (@cmci_)
downloads:kymoquant
Measure Movement directly from kymograph

Kymoquant

Quantitative analysis of ambiguous patterns in kymograph

Author

Kota Miura
Centre for Molecular and Cellular Imaging (CMCI)
EMBL Heidelberg
miura at embl dot de
Tel: +49 6221 387 404

History

  • 10-03-03 ? first version released

Source

Released under the GNU General Public License.

Requires

ImageJ ver 1.43o or higher (ImageJ, upgrade page).

Installation

Download K_kymoquant.ijm to a place where you can access easily. Install the macro by [Plugins→Macros→Install…].

Description

Measures orientation of kymograph by estimating the direction of image texture. Outputs movement velocity in pixels / frame.

(more explanation on measurement principle is planned here)

Tip: When kymograph traces are steep, analysis results become unstable since calculation of direction involves tanθ. Be sure to capture original sequence with high time resolution if possible.

Work Flow

Kymograph should be prepared by your self either by manually using stack reslicing function in ImageJ, or ImageJ Kymograph plugin.

If you want to measure full frame of the kymograph, simply apply [Plugins → Macros → Measure Velocity from Kymograph: Full Frame].

If you want to measure only part of the kymograph, then select a area by rectangular ROI tool and then [Plugins → Macros → Measure Velocity from Kymograph: ROI].

[Plugins → Macros → Scan Kymograph and Measure - Automatic Multiple Measurements] will automatically divide the kymograph into segments and sequentially measure the kymograph along the time line.

overview_kymoquant.jpg
downloads/kymoquant.txt · Last modified: 2016/05/24 12:46 (external edit)