Input/output

Input format

Config

Output format

The scans.csv file contains the columns:

  • col_dist: float, colocalization distance, if colocalized

  • colocalized bool, True if colocalized

  • color_id: integer; color of spot, 0, 1, 2 for ‘r’, ‘g’, ‘b’, respectively

  • color_str: str; color of spot, ‘r’ or ‘g’ or ‘b’

  • corrected_intensity: float, intensity corrected for crosstalk

  • dna_end_pixel: float, ending pixel coordinate of DNA (right offset)

  • dna_length_kbp: float, dna length in kbp

  • dna_start_pixel: float, starting pixel coordinate of DNA (left offset)

  • file_name: str, name of file on file system

  • frame: integer frame number

  • frame_subindex: integer, index for each spot in a scan in a frame (used for making LAP matrices)

  • intensity: integer, sum of pixel values in detected spot

  • laser_colors: str; all laser colors that were used during the experiment

  • lifetime: integer, lifetime of the track in frames

  • n_frames: integer, number of frames of scan

  • n_scans: integer, number of scans in experiment

  • scan_id: integer, identifier for scan

  • spot_id: integer, unique index for each spot (not used)

  • step_count: integer, number of steps in track (from step fitting the bleaching trace)

  • time_s: float, time in seconds

  • trace_id: integer, identifier for colocalized tracks of different colors

  • track_id: integer, a spot of a single color, tracked over time (unique after selecting a scan_id and frame)

  • x_kbp: float, distance to left bead edge in kbp

  • x_micron: float, distance to left bead edge in micron

  • x_pixel: float, x-location of spot in pixels in absolute coordinates

  • y_pixel: float, y-location of spot in pixels in absolute coordinates

Table indices and class hierarchy

The scans.csv table has several index (*_id) columns. The most useful way to think about these is as follows.

A track is a single-color spot, tracked over multiple frames in a scan. Hence, a track contains multiple spot locations; at most one spot location for each frame, although some frames might be skipped. By picking a scan_id, track_id in the table you can find each separate track that is present in the dataset. The trace_id index groups colocalized tracks together.

This data hierarchy is mirrored in the way the code is organized into classes. An Experiment can contain multiple Scans (one for each image taken); a Scan can contain multiple Traces; a Trace can contain multiple (colocalized) Tracks. A Track is a single-color spot, tracked over multiple frames.

Different physical quantities belong to different levels in this class hierarchy. Stoichiometry, for example, is a Trace attribute, but fluorophore lifetime is a Track attribute.