Parameters.md

Tethered fly pipeline parameters

This pipeline uses Nextflow and processes videos of tethered flies using APT to produce tracking output.

Data

Filepaths to directories and files used for input and output

Parameter	Description	Type
input_dir	Top level directory for experiment containing all individual fly subdirectories	string
output_dir	Directory where final results .trk, _3dres.mat will be generated. The per fly and per video results will be generated in the corresponding subfolders as found in the input, e.g., .../fly4315/C001H001S0002/C001H001S0002_c.trk	string
tmp_tracking_dir	Directory containing the intermediate results generated during the detect step	string
scratch_dir	Temp scratch directory for holding results before moving them to final destination	string
label_filename	e.g. /groups/branson/bransonlab/apt/experiments/data/sh_trn5017_20200121_stripped.lbl	string
body_axis_lookup_filename	.csv file containing fly numbers with the corresponding body axis .lbl files e.g. /groups/huston/hustonlab/flp-chrimson_experiments/fly2BodyAxis_lookupTable_Ben.csv	string
crop_regression_filename	e.g. /groups/branson/bransonlab/mayank/stephen_copy/crop_regression_params.mat	string
model_name	e.g. stephen_20200124	string
calibrations_filename	.csv file containing fly numbers with the corresponding calibration files	string
model_cache_dirname	/groups/branson/bransonlab/mayank/stephen_copy/apt_cache	string
flydata_dirname_pattern	Regex pattern for selecting the fly directories. This can be used for running the pipeline only for one or two flies for example: fly123[4,8] - selects only fly1234 and fly1238 as inputs. Default: fly[0-9]*	string
flydata_maxdepth_search	If greater than 0 it specifies how many levels to look for flydata directories under input_dir. Default: 0 (unlimitted)	integer
sideview_videoname_pattern	Filename pattern for SIDE view videos. Changing this may require settting frontview_videoname_pattern so that we process the side and front view in pairs. Default: C001*.avi	string
frontview_videoname_pattern	Filename pattern for FRONT view videos. Changing this may require settting sideview_videoname_pattern so that we process the side and front view in pairs. Default: C002*.avi	string
sideview_detect_result_suffix	Filename suffix used for SIDE view intermediated results. Default: _side	string
frontview_detect_result_suffix	Filename suffix used for FRONT view intermediate results. Default: _front	string

Detection parameters

Parameters for the detection step

Parameter	Description	Type
sideview_crop_size	Default crop size used for SIDE view. Only change this if you know how this impacts the algorithm. Default: 230,350	string
frontview_crop_size	Default crop size used for FRONT view. Only change this if you know how this impacts the algorithm. Default: 350,350	string
apt_detect_cpus	Number of CPU cores for detection. Default: 2	string
apt_detect_memory	Amount of memory for detection. Default: 30 G	string

Tracking parameters

Parameters for the tracking step

Parameter	Description	Type
apt_track_cpus	Number of CPU cores for tracking. Default: 3	string
apt_track_memory	Amount of memory for tracking. Default: 45 G	string

Container Options

Customize the Docker containers used for each pipeline step

Parameter	Description	Type
apt_detect_container	Docker container for running detect using APT. Default: public.ecr.aws/janeliascicomp/huston/apt_detect:1.1.0	string
apt_track_container	Docker container for running tracking using APT. Default: public.ecr.aws/janeliascicomp/huston/apt_track:1.1.0	string

Other Options

Other global options affecting all pipelines stages

Parameter	Description	Type
singularity_cache_dir	Shared directory where Singularity containers are cached. Default: $shared_work_dir/singularity_cache or $HOME/.singularity_cache	string
singularity_user	User to use for running Singularity containers. Default: $USER Help This is automatically set to ec2-user when using the 'tower' profile	string
runtime_opts	Runtime options for the container engine being used (e.g. Singularity or Docker). Help Runtime options for Singularity must include mounts for any directory paths you are using. You can also pass the --nv flag here to make use of NVIDIA GPU resources. For example, --nv -B /your/data/dir -B /your/output/dir
	string
lsf_opts	Options for LSF cluster at Janelia, when using the lsf profile.	string