Greetings Javier, The simple and should work way to answer your question: Plugins>Macros>Record Plugins>SynQuantSimple Fill in the GenericDialog as per your needs. Click OK. Copy and paste the code to your macro...
Reading between the lines as to why this does not work: (Someone please point to more authoritative comprehensive documentation...) The needed syntax of the second parameter (options) to the run command is generated from the GenericDialog that was aforementioned used, see <https://github.com/freemanwyz/SynQuantSimple/blob/main/src/main/java/SynQuantSimple.java>.showDialog. My understanding is that the first word of the prompt of each widget is used as the variable name in the options string. As you can see, these first words are not unique, and thus when GenericDialog is running subject to a macros call, this alignment can not be done (correctly). Thus I assume that the direct answer to your specific is that it can not be done. Reading the ReadMe at the link you provided, it states that there is an alternate plugin that takes its parameters from a file. I suspect the authors of this tool were not aware of the aforementioned requirement to get parameter passing to a macro to work. I suspect that you need to create this file and use the SynQuantBatch plugin. Enjoy, Fred On Thu, June 19, 2025 11:10 am, F Javier DÃez Guerra wrote: > Hello, > > Iâm currently developing a custom ImageJ macro to segment synapses in 2D > neuronal cultures that have been fixed and immunostained using > antibodies against pre- and post-synaptic markers. > > The SynQuantSimple plugin <https://github.com/freemanwyz/SynQuantSimple> > has proven to be highly efficient for detecting the relevant puncta. > I've found that adjusting its parameters â such as |zscore_thres|, > |MinSize|, |MaxSize|, |minFill|, |maxWHRatio|, and |zAxisMultiplier > noiseStd| â allows for effective customization to suit our image data. > > When I run the plugin manually, the results are very good with a > specific parameter configuration. However, when I try to apply those > same parameters within an ImageJ macro, /SynQuantSimple/ appears to > revert to its default settings instead. > > Is there a way to pass custom parameter values to /SynQuantSimple/ via > macro? > > Any guidance would be greatly appreciated. > > Best regards, > > Javier > > > F Javier Diez-Guerra, PhD > Servicio de MicroscopÃa Ãptica Avanzada (SMOA) > Centro de Biologia Molecular > C/ Nicolás Cabrera, 1 > UAM, Campus de Cantoblanco > 28049 Madrid > SPAIN > > Tel +34 91 196 4612 > e-mail:[email protected] > > -- > ImageJ mailing list: http://imagej.nih.gov/ij/list.html > -- ImageJ mailing list: http://imagej.nih.gov/ij/list.html
