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 thantrace_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
).