Open-3DSIM: an Open-source three-dimensional structured illumination microscopy reconstruction platform

Abstract

With optical section and defocus removal effect, three-dimensional structured illumination microscopy (3DSIM) can get a whole sight of intracellular organelle. Here, Open-3DSIM is reported as an open-source reconstruction platform with double improvement on lateral and axial resolution. MATLAB code, ImageJ version and Exe application are provided for biologists and engineers to maximize its user-friendliness and prompt its further development. Through adaptive parameter estimation and spectrum filter optimization, we demonstrate its superior performance of artifact suppression and defocus elimination over other algorithms on various specimens, under gradient signal-to-noise levels. Moreover, with the capacity to extract the dipole orientation, Open-3DSIM paves a new avenue for interpreting the subcellular structures in six dimensions.

Dark-based Optical Sectioning assists Background Removal in Fluorescence Microscopy

“…HiLo microscopy 31, 32 has a better optical section capability than WF, but it needs two images with illuminated patterns to reconstruct one image with the background removed. Furthermore, 3DSIM 11, 12 with double resolution in the xyz directions has a great background removal capability. Thus, we do the comparison between WF, Dark WF , HiLo, 2DSIM, 3DSIM, and 2DSIM processed by Dark sectioning (Dark 2DSIM ) using mouse kidney section as an example in Fig.…”

“…We firstly introduce it into polarized microscopy and do the comparison between polarized wide-field (pWF), polarized 3DSIM (p3DSIM), polarized WF images assisted by Dark sectioning (pDark WF ), and polarized 3DSIM images assisted by Dark sectioning (pDark 3DSIM ) of actin filament in mouse kidney section. Dipole orientation interpretation 11, 34 depends on the intensity ratio of WF images from different polarization angles, and defocused backgrounds change the intensity ratio of WF images, making it difficult to analyze the dipole orientation in Fig. 3(a).…”

“…Although optical approaches such as laser-scanning confocal microscopy 9 or multi-photon microscopy 10 provide enhanced optical sectioning performance, they have relatively lower temporal resolution with more photobleaching due to high doses of light. Other imaging techniques relying on the active illumination modulation and WF-based array detection, such as spinning-disk confocal, multi-focal structured illumination microscopy, three-dimensional structured illumination microscopy (SIM) 11, 12 , lightsheet microscopy 13 , or super-resolution optical fluctuation imaging 14, 15 (SOFI), also suffers from the defocused noise and lower imaging speed despite improving axial sectioning.…”

Tiled and layer-adaptive three-dimensional structured illumination microscopy based on principal component analysis

“…We used N-SIM to acquire a set of mitochondrial 3D images of bovine pulmonary artery endothelial (BPAE) cells for testing. Here we compare our method with the most novel open source algorithm Open 3D SIM 15 to verify its effectiveness in artifact removal and image quality improvement. Through the comparison in Fig.…”

A gentle palette of plasma membrane dyes

“…Anterograde transport ensures the transportation of healthy mitochondria from the soma to the axon terminals, while retrograde transport primarily facilitates the transfer of damaged mitochondria back to the soma for degradation and recycling 61,62 . Structured illumination microscopy (SIM) is suitable for long-term, super-resolution imaging of live cells as it offers higher temporal resolution yet lower phototoxicity compared to STED microscopy [63][64][65][66] . During the time-lapse SIM imaging of neurons labeled with PK Mem 555 and PK Mito Deep Red, the mitochondrial bidirectional transports within neuronal axons were monitored for over 4 hours (7600 frames) (Fig.…”