Running the GUI
If you already have the GUI running, then skip ahead to the "Using the GUI" section below
The simplest way to run mmhelper is by navigating to the mmhelper folder in your file explorer window and clicking on the windows bath file entitled "run":
Once the GUI is up and running it should look like this:
Adding a file(s) or folder to mmhelper is easy. You can:
- manually type the file(s) or folder path in to the box provided
- Select it using the button provided
- "Drag and drop" it on to the GUI
The various input options and the respective parameters required on the user interface are listed below.
N.B. If running in batch mode on a folder of images (can include fluorescence) then see the next section
- Single brightfield or phase contrast image - add the file and hit "start analysis"
- stack of brightfield or phase contrast images - add the file and hit "start analysis"
The fluorescence images can be provided in one of two ways:
- Alternating stack of brightfield/phase contrast images and their matching fluorescent images (e.g. BF/Fluo/BF/FLuo) - add the file, select "combined fluorescence" and hit "start analysis"
- Corresponding fluorescent image(s) are in a separate file (stacks if multiple frames) - add the files, select "separate fluorescence" and hit "start analysis"
mmhelper also has the capacity to run in batch mode on a data set containing multiple areas. In order to do this the files within the folder must be in one of two formats:
- All images are separate files, in which case each file must be named with the format "a_b_c.tif"
- All areas are separate stacks, in which case each file must be named with the format "a_c.tif"
Where:
- a = an identifier for the area in which the image was taken. E.g. "01" for all images in the first area of the mother machine, "02" for the second, etc.
- b = a time stamp - this allows mmhelper to stack images from the same timepoint in chronological order
- c = any further identifiers of your choice (optional)
Once you have a suitable folder, you simply add it to the interface as described and select "batch run".
If it is just brightfield/phase then you can hit "start analysis", but if your folder includes fluorescent images (see note below) then select "combined fluorescence" before starting the analysis
Note: When including fluorescent images in a folder, if using option 1 from above (individual files for each image) then the timestamps should alternate between BF/Phase and the matching fluorescent image
You also have the option of specifying where you want the output of the analysis to be saved. If this is undefined then it will be in the same folder as the input
Once the analysis has finished you can simply click on the button "open results folder" to find your results. For more information on understanding results then click here