Skip to content

Running ADAPT

Jump to bottom
Dave Barry edited this page Jan 19, 2024 · 3 revisions

ADAPT is designed to analyse greyscale image stacks - colour images should be split into their constituent channels prior to analysis.

Upon selecting CALM > Adapt > Analyse Movie from ImageJ's Plugins menu, a dialog opens for the user to specify a directory where output data and images will be stored:

ADAPT_DIR_GUI.png

Once a valid directory is provided, the user is requested to designate an image stack as the Cytoplasmic signal (the reference for segmentation) and a second stack, if any, as the Signal to be correlated:

ADAPT_SPECIFY_CHANNELS.png

The cyoplasmic signal should consist of a bright cell (or cells) against a dark background - phase contrast images, for example, will result in poor segmentation results. Any file format readable by FIJI/ImageJ/BioFormats is acceptable as input, so long as each channel is monochrome.

Finally, the user is presented with an interface, through which various parameters may be set:

ADAPT_Interface.png

Clicking Preview will generate a preview segmentation, as illustrated above for a blebbing HeLa cell expressing GFP and MLC2-RFP. When the Run button is clicked, the analysis proceeds and results are output to the specified directory.

Can't find what you're looking for? Post a question on the image.sc forum using the #adapt hashtag.

Jump to...

Clone this wiki locally