2 Four step parameter adjustment

In this wiki, we intend to provide a comprehensive guide for the readers/users to process their data, including the detailed procedures to adjust the Fidelity and Sparsity values.

STEP 0.

Set the Fixed parameters and Image property parameters according to the microscope hardware, computing system, and properties of images.

STEP 1.

Choose the initial Fidelity value according to the image SNR. We recommend starting from 1000 for high SNR images or 500 for low SNR ones. For starters, we also recommend choosing the Sparsity as one-twentieth of the Fidelity, which is to avoid over-filtering artifacts due to the inappropriately high Sparsity value.

STEP2.

Adjust the Fidelity and Sparsity downwards simultaneously with the ratio maintained. Because the Fidelity is the opposite of the xy continuity term, its reduction constrains the reconstruction with more weight on the continuity. However, unnecessary small Fidelity values may over-smooth the structures and reduce the resolution. Therefore, we need to examine the reconstruction results and terminate the downwards adjustment once image over-smoothing is apparent.

STEP 3.

Fine-tune Sparsity upwards. Large Sparsity values help us recover the high-frequency information on the one hand but also may over-filter the weak signals on the other hand. Therefore, we increase the weight of Sparsity until over-filtering artifacts emerge. Please note that adjusting the Sparsity value changes the ratio of Fidelity and Sparsity.

STEP 4.

Stop at the value of Sparsity with the right balance of resolution and minimally removing weak fluorescence signals.