Dendrites
Automatic segmentation
Track and quantify dendritic stretches across snapshots and channels.
Open-source software
SpyDen
A graphical Python toolkit for reproducible molecular and structural analysis across dendrites and spines — built to make sophisticated image analysis usable without requiring direct programming.
Synapses
Editable spine analysis
Manual or ML-assisted annotation with editable algorithmic output.
Molecules
Puncta & intensity analysis
Analyze discrete puncta and continuous molecular signals within defined compartments.
Tutorials
Learn SpyDen by watching.
Six short video tutorials from loading data through dendrite, synapse and puncta analysis to output formats.
Loading data into SpyDen ↗
Folder structure and getting your data ready.
Getting started analyzing ↗
A quick introduction to the interface and workflow.
Analyzing dendrites ↗
Dendritic segmentation and measurement workflow.
Analyzing synapses ↗
Synapse and spine analysis inside the SpyDen GUI.
Analyzing puncta ↗
Protein / mRNA puncta analysis workflow.
Understanding the output ↗
Files, formats and interpreting exported results.