Panels
How to make an analysis of your own – by describing it to an AI assistant, or by writing it – and where it lives.
Every analysis in SMAPpy is a plugin: a form of settings, a Run button, and a few lines of Python behind them. When none of the shipped ones measures what you need, you can add your own, and it behaves like any other: it has a form, it runs on the localizations you are looking at (the layer's filter, inside the ROI), it draws its figures, and it can be pinned to a tab or run per ROI.
You do not need to be a programmer. The usual way is to describe what you want to an AI assistant – "for each cluster, the number of localizations and the radius of gyration, as a histogram" – and let it write the plugin. Your plugin folder comes with the instructions an assistant needs.
SMAPpy always reads one folder of your own: Plugins > Show my plugin folder opens it, and the preferences show its path. A Python file saved there is a plugin the next time the Plugins menu or a tab's + is opened; nothing has to be installed or registered, and SMAPpy does not need a restart.
cluster_sizes.py becomes User > Cluster Sizes.Analysis/Measure/cluster_sizes.py sits beside the shipped measurements.Plugin folders of your own beyond this one – a lab's shared folder, say – are added in File > Preferences.
The tutorial Your own plugins shows the whole way, from New plugin... to a plugin an assistant changed.
Start from the example. Plugins > New plugin... asks for a name and copies a working example plugin into your folder under that name. It measures how far each localization is from its nearest neighbour, which is small enough to read and has every part a plugin needs: settings, a measurement, a figure, and numbers per ROI. The same from a terminal: smappy-plugins new "cluster sizes".
With an AI assistant that works on files (Claude Code, Codex and similar): open a terminal in your plugin folder, start the assistant there, and describe what you need – what to measure, on which localizations, what the result should look like. The folder holds AGENTS.md (and CLAUDE.md, which reads it), which tells the assistant how a SMAPpy plugin is written, so it does not have to guess. SMAPpy keeps that file up to date with the version you have installed.
With a chat assistant: paste the contents of AGENTS.md into the chat, then your description, and save the answer as a .py file in your folder.
By hand: copy _template.py (SMAPpy's example, which the menu skips because its name starts with _) and change it. A plugin is a list of settings and a run function that reads the localizations and hands back a text, numbers and figures.
Trying it. Open it from the Plugins menu and press Run. When you or the assistant change the file, open it from the Plugins menu again: the new code is read. (A section already opened in a tab keeps the code it was opened with until SMAPpy is started again.) If it does not appear, smappy-plugins check in a terminal says why – a typing error, or a missing line the program requires.
Very little. A plugin in your folder needs only to work: the program refuses a plugin that does not say whether it changes the table (changes_locs), and that is all. A help page like this one, tests, and a version number are yours to decide on. An assistant will offer them, and for a plugin you mean to keep they are worth having: a help page (cluster_sizes.md beside cluster_sizes.py) opens with the ? like any other, and a test on simulated data is how you know the numbers are right.
A plugin other people would use can become part of SMAPpy. Open a pull request at github.com/ries-lab/SMAPpy that adds it to the shipped plugins. What is shipped follows the repository's rules, which your own plugins do not have to: a help page that explains the method, tests that check the numbers on simulated data, and the house style. The repository's CLAUDE.md sets them out, and an assistant working in a copy of the repository reads it.
To share with your lab without that, put the file in a folder everyone can reach and add the folder in File > Preferences.