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Detection_Pipeline_Flow.md

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Detection Pipeline

Flow

Inputs Movie Preprocessing Detection trajec. analysis Database Management

file with meta data -> multiple meta data files ---------------------------------------------> ------------- | SQLite DB | movie with multiple arenas -> multiple movies of 1 arena -> mult trajectories -> mult. decision data -> -------------

Status: meta: open | data: done data: done data: work db: done | handler: open

Arena Numbering assignement:

Arenas are counted from the top left starting with zero. Hoprizontal first, than vertical e.g.

0 1 2 3 4 5 6 7

Meta Data needed to run the pipeline

ToDo

Done

  • Experiment (check for duplicates)

    • date_time = Column(DateTime), automated from file I/O input
    • fps = Column(Float), automated from file I/O input
    • video_file_path = Column(String), automated from file I/O input
    • experiment_type = Column(String), user input cross checked with database
    • number_of_arenas = Column(Integer), user input
    • number_of_arena_rows = Column(Integer), user input
    • number_of_arena_columns = Column(Integer), user input

  • Experimenter

    • name = Column(String), user input cross checked with database

  • Experiment Type

    • name

  • Fly (per arena)

    • is_female = Column(Boolean), user input
    • genotype_id = Column(String), user input cross checked with database
    • age_day_after_eclosion = Column(Float), user input
    • fly_attribute_2 = Column(String), user input cross checked with database
    • fly_attribute_3 = Column(String), user input cross checked with database
    • fly_attribute_4 = Column(String), user input cross checked with database
    • fly_attribute_5 = Column(String), user input cross checked with database

  • Arena (per arena, check for duplicates)

    • name = Column(String), user input cross checked with database
    • size_width_mm = Column(Float), user input new if not in db
    • size_height_mm = Column(Float), user input new if not in db
    • size_radius_mm = Column(Float), user input new if not in db
    • arena_attribute_1 = Column(String), user input new if not in db
    • arena_attribute_2 = Column(String), user input new if not in db
    • arena_attribute_3 = Column(String), user input new if not in db
    • arena_attribute_4 = Column(String), user input new if not in db
    • arena_attribute_5 = Column(String), user input new if not in db

  • Trial

    • arena_number = Column(Integer), user input
    • stimuli_01 = Column(Integer Foreign Key Stimuli table), automated
    • stimuli_02 = Column(Integer Foreign Key Stimuli table), automated
    • stimuli_03 = Column(Integer Foreign Key Stimuli table), automated
    • stimuli_04 = Column(Integer Foreign Key Stimuli table), automated
    • stimuli_05 = Column(Integer Foreign Key Stimuli table), automated
    • stimuli_06 = Column(Integer Foreign Key Stimuli table), automated
    • stimuli_07 = Column(Integer Foreign Key Stimuli table), automated
    • stimuli_08 = Column(Integer Foreign Key Stimuli table), automated
    • stimuli_09 = Column(Integer Foreign Key Stimuli table), automated
    • stimuli_10 = Column(Integer Foreign Key Stimuli table), automated

  • Stimuli

    • name = Column(String), user input cross checked with database
    • type = Column(String), user input cross checked with database
    • amplitude = Column(Float), user input cross checked with database
    • amplitude_unit = Column(String), user input cross checked with database
    • stimuli_attribute_1 = Column(String), user input cross checked with database
    • stimuli_attribute_2 = Column(String), user input cross checked with database
    • stimuli_attribute_3 = Column(String), user input cross checked with database
    • stimuli_attribute_4 = Column(String), user input cross checked with database
    • stimuli_attribute_5 = Column(String), user input cross checked with database

  • Fly Assignment to Arena

    • check the number of available flies
    • do sex by church divide (left female right male)
    • try to reserve rows for one genotype
    • allow to delete or correct flies by hand