Building chromatin traces#

Pre-processing#

Two methods are used for pre-processing localization tables.

  • filter_localizations: removes localizations that do not achieve a user-defined threshold of intensity.

  • register_localizations: applies local registration corrections to a localization table.

Building and processing trace tables#

The main method for building chromatin traces is build_traces.

Chromatin trace tables can be post-processed using multiple scripts:

  • trace_analyser: quantifies several quantities from a trace table.

  • trace_filter: applies simple filtering methods to a trace table.

  • trace_filter_advanced: applies advanced filtering to trace tables.

  • trace_assign_mask: assigns a label to traces using a user-provided mask file.

  • trace_merge: combines/merges multiple trace tables (e.g. from different replicates or FOVs) from anywhere in your file system (more flexible than trace_combinator).

  • trace_combinator: combines/merges multiple trace tables (e.g. from different replicates or FOVs) using the folder architecture of pyHiM.

  • trace_plot: script to plot one or multiple traces in 3D.

Building pairwise distance maps#

Finally, trace tables can be converted to pairwise distance matrices using either the pyHiM built-in method:build_matrices, or using an external script: trace_to_matrix).

Detailed description of methods and scripts#