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A typical example image of SIM raw data before Structured Illumination processing often shows the grating pattern that was projected onto the sample during imaging.
Processing SIM data
- Images can be taken to the ZEN analysis PC in room 2.19A for processing.
- To obtain a SIM image from your raw data go to the Processing tab (1) in the ZEN Black software. Select Structured Illumination and a dropdown menu opens. Here select Structured Illumination again (2). A menu window opens in which you can set up the Method Parameters (3). You need to do the Structured Illumination processing step for all of your sample images and the calibration bead stack.
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- Under Method Parameters press Select (1) to select the currently active image for the processing. The slices slider below the Input allows you to select, which part of a z-stack you want to process. Then choose between the Automatic and Manual processing mode in the dropdown menu (2). If the Automatic mode does not deliver the desired result e.g. produces processing artefacts in the images try switching to the manual mode to optimize the processing parameters. For the Output you can select between a SR-SIM (super-resolution SIM), Wide Field (Pseudo widefield) and DCV (deconvolved) image (3).