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Download Single Molecule Light Microscopy ImageJ Plugins
Transcript
GDSC SMLM ImageJ Plugins Table of Contents 1 Introduction........................................................................................................................7 1.1 Fitting plugins..............................................................................................................8 1.2 Results plugins...........................................................................................................9 1.3 Analysis plugins........................................................................................................10 1.4 Model plugins............................................................................................................11 1.5 Calibration plugins....................................................................................................12 1.6 Tool plugins...............................................................................................................12 2 Background......................................................................................................................14 2.1 Diffraction limit of light microscopy...........................................................................14 2.2 Approximation using a Gaussian..............................................................................15 2.3 Localisation Fitting Method.......................................................................................15 3 Installation........................................................................................................................17 3.1 Install using ImageJ2/Fiji..........................................................................................17 3.2 Install using ImageJ version 1..................................................................................17 4 ImageJ Plugins.................................................................................................................18 5 Fitting Plugins...................................................................................................................19 5.1 Simple Fit..................................................................................................................19 5.1.1 Parameters........................................................................................................19 5.1.2 Calibration.........................................................................................................20 5.1.3 Advanced Settings.............................................................................................24 5.2 Peak Fit.....................................................................................................................25 5.2.1 Imaging Calibration Parameters........................................................................26 5.2.2 Gaussian PSF Parameters................................................................................26 5.2.3 Maxima Identification Parameters.....................................................................27 5.2.4 Fitting Parameters.............................................................................................29 5.2.5 Multiple Peak Fitting Parameters......................................................................36 5.2.6 Filtering Parameters..........................................................................................37 5.2.7 Results Parameters...........................................................................................38 5.2.8 Interactive Results Table...................................................................................41 5.2.9 Live image display.............................................................................................41 5.2.10 Image examples..............................................................................................42 5.2.11 Running Peak Fit.............................................................................................43 5.2.12 Additional Fitting Options.................................................................................44 5.2.13 Interlaced Data................................................................................................45 5.3 Template Configuration.............................................................................................46 5.4 Fit Configuration.......................................................................................................47 5.5 Peak Fit (Series).......................................................................................................48 5.6 Batch Fit....................................................................................................................49 5.6.1 Configuration File..............................................................................................49 5.6.2 Running the batch.............................................................................................51 5.7 Spot Finder...............................................................................................................52 5.8 Spot Finder (Series)..................................................................................................52 5.9 Fit Maxima................................................................................................................52 5.10 Gaussian Fit............................................................................................................53 5.10.1 Maxima Identification.......................................................................................54 5.10.2 Gaussian Fitting...............................................................................................54 6 Results Plugins................................................................................................................57 Page 2 / 225
