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本数据集采用开源工具ClickPoints（clickpoints）对原代大鼠海马神经元的轴突生长锥进行了人工追踪[1]。文件"data_growth_cone_tracking.zip"中包含了在3种不同胶原浓度（0.6 mg/ml、1.2 mg/ml、2.4 mg/ml）的三维胶原水凝胶中培养3至5天的原代神经元细胞的追踪数据。追踪过程中，首先对明场图像序列（z轴高度：160 µm）计算最小与最大强度投影，并通过高通滤波与对比度增强完成预处理。图像序列的采集间隔为2分钟。数据集附带了0.6 mg/ml水凝胶中轴突的示例视频"example.mp4"，比例尺为50 µm。每个ClickPoints数据库（文件后缀为.cdb）对应单个感兴趣区域（Field of Interest, FOI）的追踪数据，追踪点的时间间隔为120秒。文件"Access_clickpoints_data.py"提供了一个极简Python脚本，可用于调取单条追踪轨迹以开展后续分析。关于ClickPoints数据库的更多操作说明，可查阅其官方文档：https://clickpoints.readthedocs.io/en/latest/。 资助声明：本研究感谢德国研究基金会（Deutsche Forschungsgemeinschaft, DFG）项目460333672——CRC1540 EBM（子项目C05与C03）提供的经费支持。 [1] Gerum R, Richter S, Fabry B, Zitterbart DP. ClickPoints: an expandable toolbox for scientific image annotation and analysis[J]. Methods in Ecology and Evolution, 2016. doi:10.1111/2041-210X.12702