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.).
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 (submitted).
Source code (Matlab): GitHub link or Google Drive, which contains the source code and the bio-format file.