This pipeline uses Nextflow and processes videos of tethered flies using APT to produce tracking output.
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 |
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 |
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 |
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 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 HelpThis is automatically set toec2-user when using the 'tower' profile |
string |
runtime_opts |
Runtime options for the container engine being used (e.g. Singularity or Docker). HelpRuntime 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 |