Embedded Files
Most of the analysis I have done uses Matlab and have now also been uploaded on my Github site. I have learned writing code by doing and with initial help from Matlab-genius postdocs in the Garcia-Parajo Lab while I was doing my PhD and later I got most of my help from Google. Below are both old and new programs that have been annotated and, if applicable, include references to original work from others. I hope you find something usefull, but please remember that most have been written to analyse something specific for me. Always double check if the code works for you as well.
Camera Calibration
Camera Calibration
A code to obtain gain, offset and readnoise values for an (EM)CCD or sCMOS camera.
Bleb segmentation
Bleb segmentation
A code to extract multi-channel intensity information along the perimeter of a bleb.
FCS
FCS
A general code to extract, analyse and normalise FCS data from a Zeiss Confocor system.
Scanning FCS
Scanning FCS
A general code to extract and correct fluorescence autocorrelation data from a scanning system.
Multi-Point camera FCS
Multi-Point camera FCS
A code to extract intensity streams from several spots on the camera that are associated to pinholes or photonic antennas.
 Multi-Point ARAP
 Multi-Point ARAP
A code to extract and fit anisotropy change from a pinhole array. Also contains a script to automatically run the spinning disk microscope.
Emission anisotropy
Emission anisotropy
A code to build the Total Intensity and Emission Anisotropy (hFRET) images and obtain region-wise extraction of the data.
Anisotropy correlation
Anisotropy correlation
This code allows the correlation between two separately hFRETting fluorophores.
Time-resolved anisotropy
Time-resolved anisotropy
This code allows the fitting of time-resolved anisotropy data (even with data overflow).
TIRF depth calibration
TIRF depth calibration
A code to automatically obtain TIRF-field depth based on bead positions in agarose from a TIRF and EPI z-stack.
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