User Tools

Site Tools


Sidebar

Top
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 @xuepan3: @palankarr @manorlaboratory Hi Raghva, We compared the results generated by IMARIS and Trackmate in ImageJ. There are some min…
About 2 days, 13 hours ago by: Kota Miura (@cmci_)

cmci_ avatar

RT @albertcardona: Plotting from your @FijiSc #python scripts, using ImageJ's internal plotting library, and with @jfreechart for prettier…
About 2 days, 14 hours ago by: Kota Miura (@cmci_)

cmci_ avatar

RT @CefapConfocal: If you struggle with image analysis, check our webpage with few ImageJ and Zen tutorials: https://t.co/9ExHi8MkL1 ps .:…
About 3 days, 10 hours ago by: Kota Miura (@cmci_)

cmci_ avatar

RT @iefforts: The cells were visualized on a Nikon AR1 or Leica SP8 confocal microscope. At least 30 cells were analysed for each condition…
About 3 days, 10 hours ago by: Kota Miura (@cmci_)

cmci_ avatar

RT @MarJungle: BigStitcher on ImageJ for 3D model reconstructions. A beta-version is available via the Fiji Updater. I am going to try this…
About 3 days, 10 hours ago by: Kota Miura (@cmci_)

cmci_ avatar

RT @ARVOtvst: New in the August issue: 25-MHz ultrasound biomicroscopy combined with #ImageJ software can be used to evaluate the opacity d…
About 3 days, 10 hours 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 05:46 (external edit)