Welcome to the ClickPoints Documentation

Click Points is a program written in the Python programming language, which serves on the one hand as an image viewer and on the other hand as an data display and annotation tool. Every frame can be annotated by a description, marked points/tracks, or marked areas (paint brush). This helps to view image data, do manual evaluation of data, help to create semi-automatic evaluation or display the results of automatic image evaluation.

Contents

• Installation
  • Python Packages
  • Update
  • Developer Version
  • Possible Errors
• General
  • Zooming, Panning, Rotating
  • Jumping frames
  • Interfaces
• Tutorial
  • Opening Files and Folders
  • Using ConfigFiles
  • Manual Tracking
  • Taking Measurements
• Modules
  • Timeline
  • GammaCorrection
  • VideoExporter
  • Annotations
  • Marker
  • Mask
  • Info Hud
• Add-ons
  • Tracking
  • Fluorescence Diffusion
  • Drift Correction
  • Cell Detector
  • Grab Plot Data
• Examples
  • Get Markers
  • Get Tracks
  • Count Animals
  • Flourescence intensities in plant roots
  • Bead Tracking
  • Simulation Visualisation
• Database API
  • Database Models
  • DataFile
• Add-on API
  • File Location
  • Meta Data File
  • Script File
  • Defining Options
  • Events
  • Commands

Note

If you encounter any bugs or unexpected behaviour, you are encouraged to report a bug in our Github bugtracker.

Citing ClickPoints

If you use ClickPoints for academic research, you are highly encouraged (though not required) to cite the following paper:

• Gerum, R., Richter, S., Fabry, B. and Zitterbart, D.P. (2016), “ClickPoints: an expandable toolbox for scientific image annotation and analysis”. Methods Ecol Evol. doi:10.1111/2041-210X.12702

ClickPoints is developed primarily by academics, and so citations matter a lot to us. Citing ClickPoints also increases it’s exposure and potential user (and developer) base, which is to the benefit of all users of ClickPoints. Thanks in advance!

Who uses ClickPoints

Here is a list of publications that used ClickPoints for their evaluation.

• Bonakdar, N., Gerum, R. C., Kuhn, M., Spörrer, M., Lippert, A., Schneider, W., … Fabry, B. (2016). Mechanical plasticity of cells. Nature Materials, 15(10), 1090–1094. https://doi.org/10.1038/nmat4689

• Braniš, J., Pataki, C., Spörrer, M., Gerum, R. C., Mainka, A., Cermak, V., … Rosel, D. (2017). The role of focal adhesion anchoring domains of CAS in mechanotransduction. Scientific Reports, 7. https://doi.org/10.1038/srep46233

• Gerum, R. C., Richter, S., Winterl, A., Fabry, B., & Zitterbart, D. P. (2017). CameraTransform: a Scientific Python Package for Perspective Camera Corrections. ArXiv http://arxiv.org/abs/1712.07438

• Richter, S., Gerum, R., Schneider, W., Fabry, B., Le Bohec, C., & Zitterbart, D. P. (2018). A remote-controlled observatory for behavioural and ecological research: A case study on emperor penguins. Methods in Ecology and Evolution. https://doi.org/10.1111/2041-210X.12971

• Gerum, R., Richter, S., Fabry, B., Le Bohec, C., Bonadonna, F., Nesterova, A., Zitterbart, D. (2018). Structural organisation and dynamics in kin penguin colonies, Journal of Physics D: Applied Physics, 51(16), 164004. https://doi.org/10.1088/1361-6463/AAB46B

• Richter, S., Gerum, R., Winterl, A., Houstin, A., Seifert, M., Peschel1, J., Fabry, B., Le Bohec, C., Zitterbart, D.P., (2018). Phase transitions in huddling emperor penguin colonies, Journal of Physics D, 51(21), 214002. https://doi.org/10.1088/1361-6463/aabb8e

• Gerlitz, N., Gerum, R., Sauer, N., Stadler, R. (2018). Photoinducible DRONPA-s: a new tool to investigate cell-cell connectivity, The Plant Journal, https://doi.org/10.1111/tpj.13918

• Pârvulescu, L. (2019). Introducing a new Austropotamobius crayfish species (Crustacea, Decapoda, Astacidae): A Miocene endemism of the Apuseni Mountains, Romania, Zoologischer Anzeiger, 279, 94–102. https://doi.org/10.1016/j.jcz.2019.01.006

• Cóndor, M., Mark, C., Gerum, R. C., Grummel, N. C., Bauer, A., García-Aznar, J. M., & Fabry, B. (2019). Breast cancer cells adapt contractile forces to overcome steric hindrance, Biophysical Journal. https://doi.org/10.1016/j.bpj.2019.02.029