[Bioc-devel] New package available: flowcatchR!

Federico Marini marinif at uni-mainz.de
Wed Oct 15 16:12:51 CEST 2014

Dear Bioconductor Community,

I'm pleased to introduce you to the new package we developed, flowcatchR!

flowcatchR is a framework for tracking and analyzing flowing blood cells 
in time lapse microscopy images.

flowcatchR provides a set of tools to analyze in vivo microscopy imaging 
data, and was developed with a focus on tracking flowing blood cells. 
flowcatchR guides throughout all the steps of bioimage processing, from 
segmentation to calculation of features, filtering out particles not of 
interest, providing also a set of utilities to help checking the quality 
of the performed operations. We address the issue of tracking flowing 
cells such as the ones in blood vessels, to categorize the particles in 
flowing, rolling, and adherent by providing a comprehensive analysis of 
the identified trajectories. The extracted information is then applied 
in the study of phenomena such as hemostasis and thrombosis development.

This is the first toolbox to offer an automated, robust and efficient 
solution for such scenarios, developed in the R/Bioconductor environment 
to leverage on advanced statistical modeling and visualization 
facilities. Our package extends the nice features already available in 
EBImage, and allows for a complete kinematics analysis. We expect this 
package to be potentially applied to a wide variety of assays founded on 
time-lapse microscopy.

Of course I would be very happy to obtain suggestions concerning 
improvements and any other feedback. Therefore, if you share a common 
interest, I encourage you to test our package for your scenarios, and 
also to recommend it to people working with time-lapse images.

flowcatchR link:

Have a nice time with the new Bioconductor 3.0 and with flowcatchR!

Best regards,

*Federico Marini, M.Sc.*
Medical Biostatistics
University Medical Center of the Johannes Gutenberg University Mainz
Institute of Medical Biostatistics, Epidemiology and Informatics (IMBEI)
Medical Biostatistics Department
Postal address: 55101 Mainz
Office and delivery address: Obere Zahlbacher Str. 69, 55131 Mainz
Phone +49 (0) 6131 17-7029
Fax +49 (0) 6131 17-472433
E-Mail: marinif at uni-mainz.de

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