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cello

Genetic circuit design automation

celltk

clusdoc

Repository associated with Clus-DoC clustering and degree of colocalization analysis

deconvolutionlab2

Java (ImageJ/Fiji) software package for 3D deconvolution microscopy

fiji

A "batteries-included" distribution of ImageJ :battery:

grafeo-dstorm-analysis-

Grafeo is Matlab based program for the analysis of a single molecule localization microscopy (SMLM) data e.g. dSTORM or PALM. It works on a single molecule coordinates rather than pixelated images. Grafeo uses various pointillist approaches previously described in the literature, e.g. Voronoi Tessellation, Delaunay Triangulation, Ripley’s function. Grafeo does not pretend to be the first to apply these functions for the single molecule data. It was developed to cope with huge amount of data to work in the batch processing mode,. Grafeo was published in Haas et al., 'Single-molecule localization microscopy reveals molecular transactions during RAD51 filament assembly at cellular DNA damage sites', Nucleic Acids Research, 2018,gkx1303, https://doi.org/10.1093/nar/gkx1303 Grafeo v1beta and its manual are far from being ideal. All the errors and inconsistencies will be corrected in the future releases. More functionalities will be added in the future release. If you have any questions please contact the author via email: [email protected] or Twitter @KalinaHaas. You can download example analysed files here: https://drive.google.com/open?id=1jLSHDbAKtExDssiNXFqeJqCCvPWm453z

matlab-storm

GUIs and functions for analyzing STORM data in MATLAB

openpiv-matlab

Matlab version of the OpenPIV project (open source Particle Image Velocimetry)

orientationj

ImageJ's plugin for directional analysis in images: color-coded analysis, distribution of orientation, vector field, keypoint detection

smeagol_mat

SMeagol: simulated single molecule microscopy, matlab part

spatiotemporal-image-correlation-spectroscopy

Spatiotemporal image correlation spectroscopy (STICS) analysis tools

thunderstorm

ThunderSTORM: a comprehensive ImageJ plugin for SMLM data analysis and super-resolution imaging

tutorials

CellProfiler tutorial pipelines and images

vbsptu

Analysis of single particle tracking data with localization errors.