1) 3D-Speckler (semi-automated 3D fluorescence Speckle Analyzer): High-throughput put fluorescence speckle/pancta analyzer. It can measure 2D/3D sizes, local background corrected integrated intensity, maximum intensity, and 2D/3D coordinates with ~1-2 nm accuracy. Details of this software can be found here (Loi, J., Qu, X., Suzuki, A.* Semi-automated 3D fluorescence speckle analyzer (3D-Speckler) for microscope calibration and nanoscale measurement. Journal of Cell Biology, 222, (4), 2023. and Lin, CC. and Suzuki, A. “Calibrating Fluorescence Microscopy with 3D-Speckler (3D fluorescence speckle analyzer)“, Bio-protocol, Vol 14, Iss 16, Aug 20, 2024).
Source code (Matlab): GitHub link or Google Drive, which contains the source code and the bio-format file.
Stand-alone version (Matlab complier): Win and Mac (Both folders contain the required specific version of Matlab runtime)
2) 3D-Aligner: A computational tool to correct for image distortion in ExM (expansion microscopy). This toolkit was integrated into the 3D-Speckler package. Details of this software can be found here ( Loi, J., Ghone D., Qu, X., Suzuki, A. “3D-Aligner: An advanced computational tool designed to correct image distortion in expansion microscopy for precise 3D reconstitution and quantitative analysis“, Communications Biology, 7, 1325, (2024). Original bioRxiv version is available here. and Hsiao, WY., Ghone, D., Suzuki, A. “Correcting image distortion in expansion microscopy using 3D-Aligner“, Bio-Protocol, in press)
Source code (Matlab): GitHub link or Google Drive, which contains the source code and the bio-format file.