Introduction
Course Overview
 
The Trainer
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Dr. Jan Brocher -  BioVoxxel


BioVoxxel was founded in 2012 by Dr. Jan Brocher and since then offers widely accepted individualized workshops in image proper image integrity and publication figure creation, image analysis and analysis automation for undergraduates, PhD students and PostDocs in life sciences worldwide.

These courses understandably transmit in-depth methodologies according to high scientific standards to enable researchers to successfully apply those to solve individual image analysis challenges and create publication figures efficiently.

Besides teaching, BioVoxxel offers customized trainings, 1:1-coaching sessions, automated solutions and customized programming of image processing and analyses tools challenges for customers as well as scientific illustration services.


Expertise

  • Bio-Image Analyst with expertise in scientific image analysis since 2010
  • Until 2025 over 400 live workshops for over 5000 students delivered
  • PhD in Molecular Biology
  • 10 years experience in international academic science
  • Experience in very diverse light microscopy techniques
  • Professional teaching as freelance scientific trainer since 2012
  • Scientific image analysis software developer since 2013
  • Bio-Image analysis consultant for academia and industry since 2013
  • Programming experience: IJ Macro, Java, Groovy, Python

This courses teaches you the proper usage of open source scientific image analysis tools but it would not be possible without the tools themselfs and the great masterminds behind those tools that foster the constantly updated possibilities in the huge universe of scientific image analysis.

Further more, it is not for granted that those publically funded tools are handed for free to the community and to scientists, since a huge amount of money originating from different science funding grants and organizations are involved in the development of such software.

Please give something back by properly citing those tools if you use them for your image analysis to produce published results.


Fiji / ImageJ

  • Schindelin, J., Arganda-Carreras, I., Frise, E., Kaynig, V., Longair, M., Pietzsch, T., … Cardona, A. (2012). Fiji: an open-source platform for biological-image analysis. Nature Methods, 9(7), 676–682. doi:10.1038/nmeth.2019

  • Schneider, C. A., Rasband, W. S., & Eliceiri, K. W. (2012). NIH Image to ImageJ: 25 years of image analysis. Nature Methods, 9(7), 671–675. doi:10.1038/nmeth.2089

Trainable Weka Segmentation

  • Arganda-Carreras, I., Kaynig, V., Rueden, C., Eliceiri, K. W., Schindelin, J., Cardona, A., & Sebastian Seung, H. (2017). Trainable Weka Segmentation: a machine learning tool for microscopy pixel classification. Bioinformatics, 33(15), 2424–2426. doi:10.1093/bioinformatics/btx180

LabKit

  • Arzt, M., Deschamps, J., Schmied, C., Pietzsch, T., Schmidt, D., Tomancak, P., … Jug, F. (2022). LABKIT: Labeling and Segmentation Toolkit for Big Image Data. Frontiers in Computer Science, 4. doi:10.3389/fcomp.2022.777728

TrackMate
  
  • Ershov, D., Phan, M.-S., Pylvänäinen, J. W., Rigaud, S. U., Le Blanc, L., Charles-Orszag, A., … Tinevez, J.-Y. (2022). TrackMate 7: integrating state-of-the-art segmentation algorithms into tracking pipelines. Nature Methods, 19(7), 829–832. doi:10.1038/s41592-022-01507-1

  • Tinevez, J.-Y., Perry, N., Schindelin, J., Hoopes, G. M., Reynolds, G. D., Laplantine, E., … Eliceiri, K. W. (2017). TrackMate: An open and extensible platform for single-particle tracking. Methods, 115, 80–90. doi:10.1016/j.ymeth.2016.09.016
SNT

  • Arshadi, C., Günther, U., Eddison, M., Harrington, K. I. S., & Ferreira, T. A. (2021). SNT: a unifying toolbox for quantification of neuronal anatomy. Nature Methods, 18(4), 374–377. doi:10.1038/s41592-021-01105-7   

  • Ferreira, T. A., Blackman, A. V., Oyrer, J., Jayabal, S., Chung, A. J., Watt, A. J., … van Meyel, D. J. (2014). Neuronal morphometry directly from bitmap images. Nature Methods, 11(10), 982–984. doi:10.1038/nmeth.3125