SynActJ | BIII

SynActJ (Synaptic Activity in ImageJ) is an easy-to-use fully open-source workflow that enables automated image and data analysis of synaptic activity. The workflow consists of a Fiji plugin performing the automated image analysis of active synapses in time-lapse movies via an interactive seeded watershed segmentation that can be easily adjusted and applied to a dataset in batch mode. The extracted intensity traces of each synaptic bouton are automatically processed, analyzed, and plotted using an R Shiny workflow.

has function

Neuron image analysis

has topic

has biological terms

Additional keywords

Entry Curator

Post date

03/21/2023 - 14:26

Last modified

03/22/2023 - 09:39

Workflow steps

Step 1: Maximum intensity projection

Fiji

Image processing

Step 2: Laplacian of Gaussian for detection

Log3D

Feature enhancement

Step 3: compute region of interest by marker controlled watershed

MorphoLibJ

Watershed segmentation

Step 4: Measure mean signal per ROI

Analyze Particles

Object feature extraction

Step 5: Analyze and filter measure over time

Shiny - R package

Frequency analysis

Download Page

https://schmiedc.github.io/SynActJ/

Documentation Link

https://schmiedc.github.io/SynActJ/

Reference Publication Link

https://doi.org/10.3389/fcomp.2021.777837

Usage Example Link

https://doi.org/10.5281/zenodo.5644945

has comparison

https://www.frontiersin.org/articles/10.3389/fcomp.2021.777837/full#supplementa…

attribution instructions

Schmied C., Soykan T., Bolz S., Haucke V., Lehmann M. SynActJ: Easy-to-Use Automated Analysis of Synaptic Activity. Frontiers in Computer Science 3 (2021) doi: https://doi.org/10.3389/fcomp.2021.777837