An intrinsic cytoskeletal oscillator establishes neuronal polarity

Data and analysis code accompanying the manuscript "An intrinsic cytoskeletal oscillator establishes neuronal polarity". 

The study shows that the neuronal soma acts as a central organiser of axon–dendrite polarity through a soma-initiated, Arp2/3-driven actin oscillator: periodic somatic actin waves remodel a global actomyosin network, transiently relax myosin-II contractility at a single neurite tip, and bias that neurite toward axon fate. Once stabilised by microtubules, the nascent axon escapes Arp2/3 dependence while sustained actomyosin activity keeps the remaining neurites as dendrites.

What this record contains

SourceData.zip — per-figure Excel workbooks (Figures 1–5) holding the numerical values, units, n, and grouping variables behind every plotted quantification.

Fig##.zip and EDFig##.zip — raw representative microscopy files (DeltaVision .dv, Zeiss .czi, TIFF, and IMOD .rec electron tomograms) corresponding to all main and Extended Data figure panels, named so that the panel reference is the file-name prefix (for example Fig.3f_… or EDfig.4d_…).

Custom_scripts_Arp3_neuronal_polarization_2026.zip — full set of custom analysis code that turns the raw data into the published quantifications. Organised by figure: an R / R Markdown notebook for every quantitative panel (Fig 1–5 and ED Fig 1–12) under figures/, parameterised analysis templates under templates/, small R utilities under helpers/, and ~70 Fiji/ImageJ macros and Jython scripts under ImageJ_macros/ that preprocess raw imaging data into the CSVs consumed by R. Includes a shared kymograph post-processor (_shared/Proc.py) and per-figure README files. Requires R 4.0.2 with the package set listed in the bundled README, Fiji ≥ 1.53 with EZColocalization, Multi Kymograph, KymoResliceWide, and ComDet plugins. The scripts are mirrored in Arp3_neuronal_polarization_2026. 

IJ_NeuriteGrowthScript.zip — Fiji/ImageJ (Jython) scripts NeuriteKymoGeneration.py and NeuriteKymoAnalyzer.py for multi-channel kymograph generation and automated neurite-tip / intensity analysis.

IJ_NeuriteGrowthScript_DEMO.zip — a self-contained demo dataset (two example movies, ROI sets, pre-computed kymographs and reference results_*.csv outputs) for end-to-end verification of a local Fiji install.

Biological and technical scope

Mouse (Mus musculus, C57BL/6 background) primary hippocampal and cortical neurons, embryonic stages E12.5–E17.5, imaged at DIV1–3. The Arp3 knockout (KO) is a CNS-wide conditional Actr3 deletion (Nestin-Cre tg/-, Actr3 fl/fl); wild-type littermates are WT. Imaging modalities span in utero electroporation followed by live cortical-slice confocal, DeltaVision wide-field deconvolution of dissociated cultures, Zeiss LSM 880/980 (including Airyscan 2) confocal, photoactivated Rac1 optogenetics (Andor spinning-disk and Zeiss LSM 980), and FEI Tecnai G2 20 dual-axis electron tomography (200 kV, SerialEM). Acquisition dates span 2013–2025; calibration metadata is preserved inside each file's native header. A complete folder map, probe and fluorophore glossary, filename-suffix glossary, imaging-setup summary, and ethics statement are provided in the bundled README.md.

Software and code

The Fiji/ImageJ scripts are also mirrored at IJ_NeuriteGrowthScript— check there for the latest version and any post-publication fixes. Scripts require Fiji with the KymoResliceWide plugin; see installation.md inside the zip.

License

Data and figures are released under Creative Commons Attribution 4.0 (CC-BY 4.0). The Fiji/ImageJ scripts carry their own LICENSE file inside IJ_NeuriteGrowthScript.zip; please consult it before redistribution.

How to cite

Please cite this Zenodo record (DOI 10.5281/zenodo.20118606) together with the associated manuscript. The manuscript was not preprinted; the journal DOI will be added on acceptance.

Contact

Frank Bradke — DZNE Bonn — [e-mail]-Chen Lin — DZNE Bonn — [e-mail].