BioImage Analysis

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Events
Upcoming
Past

The support of bioimage analysis provided by Math-Clinic includes (but not limited to):

  • image analysis techniques;
  • software tools/plugins usage;
  • programming languages;
  • script/macro writing;
  • workflow design and buildup;
  • user-specific analysis tools/code deliverables.

We offer 2 types of service:

  • 1-to-1 support and collaboration through individual appointments;
  • organizing events such as training courses and workshops

For any question regarding bioimage analysis, please feel free to contact our service partner Qi Gao (qi.gao@biologyquant.un@i-heidelberg.de). You are also welcome to join the Math-Clinic Bioimage Analysis mailing list.


Courses & Workshops

[SS 2017] Workshop: BioImage Analysis using ImageJ/Fiji, ilastik and KNIME

Jun. 19 - 21, 2017. [ course page ]
The topics range from basic concepts and principles of bioimage analysis to hands-on practices on how to use popular software tools and integrate them into your workflow.

[SS 2017] Course: Introduction to bioimage analysis using Fiji

May 12, 2017. [ course page ]
This is a special course for HBIGS PhD/Master students.

[WS 2016/17] Course: Advanced topics in bioimage analysis

Jan. 20 - Feb. 24, 2017. [ course page ]
The course consists of 6 tutorials on different topics: (1) colocalization; (2) image segmentation; (3) correspondence problems; (4) ImageJ macro language; (5) tracking; and (6) advanced image processing.

[WS 2016/17] Microscopy image analysis course

Oct. 11-12, 2016. [course page]
The course gives an introduction into the field of microscopy image analysis for cell biology and the use of software tools for automated processing of image data. This course is a joined event organized by HD-HuB and CellNetworks MathClinic.

[SS 2016] Course: Introduction to bioimage analysis and ImageJ/Fiji

Jul. 21, 2016. [ course page ]
The course includes theoretical and practical aspects: (1) basic concepts and principles of digital image processing; (2) hands-on practices on how to use Fiji for daily basic image analysis and image data quality evaluation.

[SS 2016] ilastik workshop

Jul. 11-15, 2016. [agenda]
This workshop is jointly organized by IWR and CellNetworks MathClinic.

ilastik training

Dec. 5, 2014. [agenda, slides, data, ilastik]
This event gathered those who have been to ilastik workshop(s) or talk(s) before and also know their interests for a more in-depth hands-on training. After three common sessions, we had parallel sessions in groups for specific interests, followed by an own data session.

Software training on Fiji basics

Oct. 29, 2014. [course materials]
It offered hands-on practices on how to use Fiji for daily basic image manipulations and image data quality evaluation.

2nd Math-Clinic BioImage Analysis Workshop: Fiji and KNIME

Oct. 15-17, 2014. [ workshop page, textbook, materials ]
It introduced some insights to two different open source software tools in tackling 3 common bioimage analysis problems: 2D counting, 2D+t tracking, and 3D colocalization. Participants were guided step by step to perform analysis and measurements, using both tools for comparisons.

This workshop was jointly organized by CellNetworks Math-Clinic and ViroQuant-CellNetworks RNAi Screening Facility.

Training: Fiji - Getting Started

Mar. 27-28, 2014. [ course page, slides1, slides2 ]
It offered hands-on practices on how to use Fiji for daily basic image manipulations and image data quality evaluation. In the last session, each participant brought his/her own image data, and discussed together for possible solutions using the techniques introduced during the course.

1st Math-Clinic Bioimage Analysis Workshop: Fiji and ilastik

Jan. 30-31, 2014. [ workshop page, textbook ]
It introduced some insights to two different open source software tools in tackling three common bioimage analysis problems: counting, tracking, and colocalization. Participants were guided step by step to perform analysis and measurements, using either both tools individually (for comparisons) or in a combined manner.

Tutorials

  • Deconvolution in Microscopy. [slides]
  • Fiji plugin Particle Tracker 2D/3D. [slides]
  • Fiji BioVoxxel Toolbox for extended (basic) functionalities. [slides]
  • Fiji Gel Analyzer for analyzing gels and western blots. [slides]
  • Fiji Coloc2 plugin for intensity-based colocalization analysis. [slides]
  • Fiji Squassh plugin for object-based colocalization analysis. [slides]
  • Fiji TrackMate plugin for 2D/3D time series tracking and analysis. [slides]

Other resources

Books