SynQuant for batch processing in ImageJ

This repository extends the SynQuant Fiji plugin with two additional commands, "SynQuantSimple" and "SynQuantBatch". It only works with single-channel images. However, this makes it easier to integrate into other software tools in the Fiji ecosystem, like SynBot, which has its own functions to merge results from different channels. For more details about SynQuant, please visit the main repo.

SynQuant for single channel

This is the simplified version that processes a single channel. We support 3D images with multiple z-slices. SynQuant will automatically read the current image as input. Users will be asked to set parameters and adjust z-scores after initial detection.

SynQuant for batch processing

This version allows using a configuration file as input to run SynQuant in batch. User interaction is not needed.

For example, in ImageJ scripts, for each current image, use

run("SynQuantBatch", "C:\\param.txt");

The configuration file looks like

zscore_thres=2
MinSize=10
MaxSize=200  
minFill=0.5  
maxWHRatio=4
zAxisMultiplier=1
noiseStd=20

The meaning of these parameters can be found in the documentation of SynQuant.

If no configuration file is specified, a dialogue will be prompt for you to specify the file.

Other choices for batch processing

For processing large amounts of data, another choice is to call SynQuant Java classes directly from MATLAB. An example is given here. Note that this only contains a subset of the features of the Fiji plug-in, and does not provide a GUI. For a smaller amount of images, it is better to use the Fiji plug-in.

You may also try to call SynQuant using the Python-ImageJ interface PyImageJ, but we have not tested that yet.

Reference

[1] Yizhi Wang*, Congchao Wang*, Petter Ranefall, Gerard Joey Broussard, Yinxue Wang, Guilai Shi, Boyu Lyu, Chiung-Ting Wu, Yue Wang, Lin Tian, Guoqiang Yu. (2020). SynQuant: An Automatic Tool to Quantify Synapses from Microscopy Images, Bioinformatics, 36(5), 1599–1606