Batch Mode

1. To run ADAPT in batch mode, select CALM > Adapt > Analyse Batch from the ImageJ/FIJI Plugins menu.
2. The user is then prompted to "select a directory for the reference channel". The selected directory should contain a series of TIF stacks, each representing the cytoplasmic signal of the cells to be analysed.
3. A second directory may then be selected, containing a series of TIF stacks representing any signal to be correlated. If there is no signal to be correlated (that is, there is only one channel to be analysed, the cytoplasmic signal), then simply cancel this second dialog.
4. The user will then be presented with the same GUI described here to specify parameters for the analysis (the first TIF stack in the specified directory is loaded for the preview).
5. On clicking Run, ADAPT will proceed to analyse all files in the specified directory. If two channels are being analysed, it is important to ensure that the naming of files in the two input directories is consistent, so that the correct Cyto stack is paired with the correct Sig stack.