Documentation of the sdt python package#

This package contains various tools to deal with data from fluorescence microscopy.

Overview#

  • Handle regions of interest (ROIs) is possible by means of the sdt.roi module.

  • Deal with multi-color data (channel registration, colocalization, codiffusion, frame selection according to excitation type, …) with help of functions featured in the sdt.multicolor module.

  • Determine parameters related to the motion and diffusion of single molecules (mean square displacements, diffusion coefficients, …) from tracking experiments using functionality provided by the sdt.motion module.

  • Analysis of fluorescent molecule brightness can be done with help of the sdt.brightness module.

  • The sdt.io module includes support for reading and writing data from and to files in various formats.

  • Perform changepoint detection using the sdt.changepoint module.

  • The sdt.spatial module allows for saving dealing with spatial aspects of data such as determining whether there are near neighbors, interpolating missing features in tracking data and calculating the area of a polygon.

  • Analyze single molecule FRET data using the sdt.fret module.

  • Process raw images (e.g. background subtraction) with help of the sdt.image module.

  • Using the sdt.flatfield module, flat field correction of image and localization data can be achieved.

  • The sdt.loc package allows for localization of fluorescent features in images. To that end, several algorithms are provided (sdt.loc.daostorm_3d, sdt.loc.cg), which all share a similar API. Additionally, sdt.loc.z_fit allows for determining the z position of features from astigmatism.

  • The sdt.nbui module contains GUIs to embed into Jupyter notebooks.

  • With help of the sdt.sim module, fluorescence microscopy data can be simulated.

  • The sdt.funcs module contains classes for creation of step functions and eCDFs as well as some special functions like Gaussians and sums of exponentials.

  • Plot data with methods from sdt.plot.

  • Fitting routines are available in the sdt.optimize module.

  • Some helpers for writing new code can be found in sdt.helper and sdt.config.

List of changes#

See the Change log for a list of changes between software versions.

Table of contents#

Indices and tables#