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EMBL BioImage Data Analysis

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cmci_ avatar

RT @martinjones78: Save the date! October 20th, @TheCrick Bioimage Analysis Symposium, registration opening in April #CBIAS https://t.co/6H
About 20 hours, 25 mins ago by: Kota Miura (@cmci_)

cmci_ avatar

A new data set in the NEUBAIS-@zenodo_org collection, contributed by @volker_b @NEUBIAS_COST https://t.co/FLx3q2hqM6
About 1 day ago by: Kota Miura (@cmci_)

cmci_ avatar

RT @EuroBioImaging: Last chance to present your bioimaging analysis work at 4th NEUBIAS conference 👇 https://t.co/D4jfEVfWGo
About 4 days, 2 hours ago by: Kota Miura (@cmci_)

cmci_ avatar

RT @f_levet: You have until next monday to submit an abstract to the @NEUBIAS_COST Symposium. It's your last chance ! Go go go !
About 4 days, 4 hours ago by: Kota Miura (@cmci_)

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Bioimage Analysis Lunch Heidelberg, Jan 2020 https://t.co/6FcCNzu1QJ
About 4 days, 4 hours ago by: Kota Miura (@cmci_)

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RT @Datascience__: DL@MBL: Deep Learning for Microscopy Image Analysis https://t.co/DT25zxxaRn #DeepLearning
About 5 days, 2 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)