User Manual
The installation process is the same either using ImageJ or Fiji. Along the text, both will be referred as ImageJ.
For ImageJ users: 1 - Download the last version of iSBatch.
2 - Save it in your ImageJ Plugins folder (e.g. ...ImageJ/plugins/jar/).
3a - Start ImageJ and you should see a new menu (Plugins>Single Molecule Biophysics>iSBatch)
3b - If ImageJ is open, select on ImageJ panel Help>Refresh Menus
Fiji users can use the automatic installer. Instructions here.
iSBatch expects a specific folder structure to work. A Field of view - FoV (represented by the icon 
) is a folder with images from a certain region in the microscope. All images taken from that area are from the same Field of View, irrespective to color or time in space.
A collection of Fields of View is called "Sample" ( 
). You may thing of Samples like a collection of images acquired under the same conditions, e.g. laser intensity, exposure time;
A collection of Samples defines an Experiment (
).
Choose the database file or create one. When selecting "Choose database", you can create a new one writing the desired name in the panel. The database will be automatically saved.
Together with the database, iSBatch creates a folder database_files. All created files will be saved in that folder. The database file can be moved but it is important to keep the database_files folder in place.
iSBatch will either create a empty database or load the current data. In any moment, the user can add new nodes to any part of the tree. Be aware with "Time Sampling" and "Rapid Acquisition" experiment types. There types are interpreted differently within iSBatch. Do not mix them. Create as many experiments as needed.
