Start an evaluation
This tutorial will exemplify basic rapidSTORM usage by showing
how to convert an Andor SIF acquisition to a super-resoluted image
with rapidSTORM. We will load an Andor SIF file, characterize the
optics by giving a pixel size and the PSF full width at half maximum,
give a target image resolution and start an evaluation.
- Start rapidSTORM via the icon in the Start menu
- Select the input file by dragging & dropping it from a
Windows Explorer window to the Input file
field (
. - Set the input pixel size by entering the value in the Size of one input pixel
field (
). - Enter the full width at half maximum of your point spread function into
the PSF FWHM field (
. You can estimate this value from
the numerical aperture of your microscope by the approximation λ / 2 NA, where λ is
the detection wavelength and NA the numerical aperture of your objective. - Show the options of the image display output by clicking on it
(
) in the output option tree. - Optionally change the resolution of the result image by changing the resolution
fields (
). - Start the computation by clicking the Run button (
).
After you finished starting the evaluation, a new tab will appear in the job tab bar, and a new window will be opened. Continue with the next task: Manage an evaluation.
Manage an evaluation
This tutorial shows how to interpret the job window and to modify the output image.
We assume you have started a job, as described in the Start an evaluation
tutorial.
- Enhance the image contrast by raising the Extent of histogram normalization value to 0.5. Note how the intensity key next to the image display window changes.
- Filter out low-intensity localizations by checking the box next to Minimum localization strength and entering a value of 4500. Filtering out weak localizations reduces background noise and enhances the image resolution slightly, but reduces the number of localizations available for image construction.
- Change the colour code by changing Color palette for display to Vary hue with coordinate value. The color of the image now shows the X coordinate, resulting in a rainbow-coloured image.
- Change the hue-producing coordinate by changing Coordinate to vary hue with to emission strength. The colour code would now display the intensity of each localization, but stays grey because the range is not set.
- Change the Color range fields at the lower right end of the result image window to 5000 and 30000 by entering each value and pressing enter.
- Close the job by pressing Close job. The image window will stay active until it is closed.