Tracking data of neuronal growth cones in 3D collagen hydrogels

Axonal growth cones of primary hippocampal rat neurons were manually tracked using the open source tool "clickpoints" [1].The file "data_growth_cone_tracking.zip" contains data of primary neuronal cells cultured for 3 to 5 days in 3D collagen hydrogels with three different collagen concentrations (0.6 mg/ml, 1.2 mg/ml, 2.4 mg/ml).For tracking, minimum and maximum intensity projections of bright field image stacks (z-height: 160 µm) were computed and prepocessed with high-pass filtering and contrast enhancement. Image stacks were recorded every 2 minutes.An exemplary video of axons in a 0.6 mg/ml hydrogel is provided as "example.mp4", scale bar: 50µm.Each clickpoints database (".cdb") yields data from a single Field of Interest (FOI). Time interval between tracking points is 120 seconds.The file "Access_clickpoints_data.py" provides a minimalistic python script that allows to access single tracks for further analysis.More information on how to handle clickpoints databases can be found in the documentation: https://clickpoints.readthedocs.io/en/latest/ Funding: We gratefully acknowledge the financial support by the German Research Foundation (DFG), project 460333672 - CRC1540 EBM (subprojects C05 and C03). [1]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