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High-throughput multi-target fly tracer and sleep analyser

features

1. introduction:

   This program convert fly video to coordinates by tracking, and then convert coordinates data to sleep data, and at last analyze sleep in a series of parameters about sleep.

2. Pipeline:

    (1) video preparation and background initiation
   
    		v
   
    (2.1) configure ROI of fly-containing tubes
   
    		v
   
    (2.2) tracing flies with multi-thread on CPU
   
    		v
   
    (3.1) configure time schedule etc.
   
    		v
   
    (3.2) analysis of sleep parameters
   
    		v
   
    (4) analysis summary and curve plot
   

Step (1):

Step (2):

time schedule, group name & indices, dead fly indices

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information of files and directories in this project

integrated sleep program

[Dependencies]
	cv2.pyd, numpy, matplotlib;
	opencv_core2413.lib, opencv_highgui2413.lib, opencv_imgproc2413.lib, opencv_ffmpeg2413_x64.lib
[Content]
	including fly tracer binary programs, configuration tools
	main entry: launch.py
	based on Python-2.7, which gather all programs in pipeline togather

autodetect

[Dependencies]
	opencv_core2413.lib, opencv_highgui2413.lib, opencv_imgproc2413.lib, opencv_ffmpeg2413_x64.lib
[Content]
	<autodetect> pretrained ANN parameters, involving in semi-auto detection of tubes containing traced flies.
	<autodetect/glasstubes - pixels> Scripts that build model network and create dataset during model training.

SingleTracer_v4.0

[Dependencies]
	opencv_core2413.lib, opencv_highgui2413.lib, opencv_imgproc2413.lib, opencv_ffmpeg2413_x64.lib
[Content]
	OpenCV-based multi-thread tracer of fly activities.
	v4.0 is the previous stable version, which is reserved here as a backup.

MSleepSummariser_20160616

[Dependencies]
	numpy, matplotlib, pandas, tkinter
[Content]
	python GUI that summarizes the sleep analysis of a tracing result.

other scripts .py

[Dependencies]
	numpy, matplotlib, cv2.pyd
[Content]
	> checkDataValid_0909.py: check common bugs hidden in configure or old data - an experience-based debug script.
	> cleanSleepEpisode_0910.py: convert raw sleep episode data into filered summarized data table.
	> clearDavCvt_181018.py: clear dav files that is converted into avi, while email report at specific time interval.
	> compareEpisodes.py && compareSleepLevel.py: calculating differences of sleep episodes and level between two groups.
	> configDeath_1020.py: interactive configuration GUI that filters dead flies and defines time interval to be calculated.
	> configOrder_1020.py: index every fly to its corresponding group, which is further used in statitical comparison task.
	> configTime_1020.py: set the offset time to nearest CT-0, and output a series of time schedule used in a tracing task. 
	> exportActogramSpeed_180604.py: downsampling speed data of tracing, which then could be used in circadian analysis.
	> gatherAllDav.py and grouping.py: path utilities to recursively enumerate and collect all dav files in one path.
	> plotLights.py: based on output from instance defined in MLightMonitor.hpp, it will draw the light condition schedule.
	> readEegEvent_190116.py: input EEG sleep event table, output curves of sleep events, including REM, NREM, and WAKE.
	> speed2wake_181226.py: input tracing speed data, output curve of waking number in every 30min interval
	> statSurvival_180505.py: statistical analyses of survival rate in a starvation resistance or lifspan assay.
	> tracePlayer_v0730.exe && tracePlayer-queue_v0801.exe: replay of tracing coordinates generated from singleFlyTracer, which directly show replay in a window or output a series of labeled images for specified time range, correspondingly.

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Other notes

白色胶条：5孔（含边界）=44mm