Actin Segmentation Modulation

The Matlab code I wrote to compute speckle modulation.

Quick start

This repository implements speckle modulation computation for fluorescent speckle microscopy image data in Matlab. See DEPENDENCIES.md for the Image Processing Toolbox requirement.

Repository contents

• getModulation.m -- the main function; computes the number of speckles in a region of interest and their mean modulation.
• fsmPrepScaleSpace.m, fsmPrepSubstructMaxima.m, fsmPrepMainSecondarySpeckles.m, fsmPrepCheckDistance.m, fsmPrepCheckInfo.m, fsmPrepConfirmSpeckles.m -- scale-space speckle detection.
• batch.m, candsRoi.m, prepareRowData.m, selectRectangle.m, selectRegion.m, Gauss2D1.m -- supporting utilities.
• gui/ -- a screenshot of the fsmDetection GUI.
• results/ -- a speckle density example output.
• License: see LICENSE -- research/educational use.

About

My work on speckle modulation for the publication:

Mike Adams, Alex Matov, Daphne Yarar, Steph Gupton, Gaudy Danuser, Clare Waterman "Signal Analysis of Total Internal Reflection Fluorescent Speckle Microscopy and Wide-Field Epi-Fluorescence FSM of the Actin Cytoskeleton and Focal Adhesions in Living Cells" (2004).

https://researchgate.net/publication/8204587_Signal_analysis_of_total_internal_reflection_fluorescent_speckle_microscopy_TIR-FSM_and_wide-field_epi-fluorescence_FSM_of_the_actin_cytoskeleton_and_focal_adhesions_in_living_cells