Algorithm Enables Faster Super-Res Structured Illumination Microscopy

Researchers from China’s Xi’an Jiaotong University have created a novel algorithm that delivers super-resolution images 80 times faster than the current standard imaging method for structured illumination microscopy, addressing the significant computing burden of complex super-resolution structured illumination microscopy (SR-SIM) workflows.

SR-SIM is an outstanding method for visualizing the subcellular dynamics in living cells, achieving rapid, optically sectioned (OS), super-resolution (SR) observation with hundreds to thousands of time points, which are the number of superresolution frames for continuous imaging.

However, the reconstruction algorithm for OS-SR-SIM employs a complex workflow and requires a large number of calculations, essentially negating potential for real-time imaging. In practice, 4 to 8 seconds are required to reconstruct a single SR image of 1024×1024 pixels.  Microscope operators must first use the widefield mode to navigate the promising field-of-view for their investigations, then switch to the SR-SIM mode to acquire the raw images for SR-SIM, and then wait a long time to observe a single SR image after dedicated postprocessing. The disjointed workflow of SIM setup hinders widespread application of SR-SIM among biologists.

Currently, parallel computing tools such as GPUs can be employed to accelerate the SR reconstruction, but the result is limited to a modest raw image size.

A study published recently in Advanced Photonics details an algorithmic solution to these workflow and image size limitations. Called Joint Space and Frequency Reconstruction (JSFR-SIM), the algorithm addresses both reconstruction speed and the limitation known as the “missing cone problem,” which arises due to missing data in a spatial frequency domain along the rotation axis. By combining a spatial domain processing technique with OS-SR-SIM implemented in the frequency domain, the method achieved improved image reconstruction speed plus suppression of the fuzzy background in images of thick cells.

The execution speed of the reconstruction is 80 times faster than the widely used Wiener-SIM. "Critically, the speed increase does not come at the expense of image quality,” according to the paper.

To assess the capability of JSFR-SIM in biological imaging, the authors experimentally observed the microtubule cytoskeleton in a prepared slide of thick COS-7 cells. The strong background fluorescence of the cytoskeleton in the widefield images was effectively suppressed in results using JSFR-SIM. Additionally, the image quality and spatial resolution of JSFR-SIM were virtually identical to that of the conventional Wiener-SIM, recovering the dual-color 3D dynamics of thick COS-7 cells. “Therefore, JSFR-SIM is capable of producing high-quality SR images with exceptional spatial resolution at a significantly more rapid reconstruction speed and, importantly, the increased speed does not come at the expense of the spatial resolution or sectioning capability,” the authors write.

JSFR-SIM is compatible with various SIM modalities as it shares the same hardware setup as the conventional 2D-SIM, according to the paper. “Thus, it can be easily applied in many new SIM modalities including adaptive-optics-aided SIM (AO-SIM), polarized SIM (pSIM), and grazing incidence SIM (GI-SIM) to release the computing burden in either online or offline ways, even when imaging thicker samples.”

The authors believe the breakthrough will improve the work efficiency of biologists and facilitate SR-SIM as a routine tool in biomedical laboratories.