# set switches and parameters
parser = argparse.ArgumentParser(
prog='python mm3_Compile.py',
description=
'Identifies and slices out channels into individual TIFF stacks through time.'
)
parser.add_argument('-f',
'--paramfile',
type=str,
required=True,
help='Yaml file containing parameters.')
namespace = parser.parse_args()
# Load the project parameters file
mm3.information('Loading experiment parameters.')
if namespace.paramfile:
param_file_path = namespace.paramfile
else:
mm3.warning('No param file specified. Using 100X template.')
param_file_path = 'yaml_templates/params_SJ110_100X.yaml'
p = mm3.init_mm3_helpers(param_file_path) # initialized the helper library
# define variables here
source_dir = p['experiment_directory']
dest_dir = os.path.join(source_dir, 'TIFF')
file_prefix = p['experiment_name'] # prefix for output images
file_name_filters = p['metamorphToTIFF']['file_name_filters']
if not os.path.exists(dest_dir):
os.makedirs(dest_dir)
parser = argparse.ArgumentParser(prog='python mm3_Track.py',
description='Track cells and create lineages.')
parser.add_argument('-f', '--paramfile', type=str,
required=True, help='Yaml file containing parameters.')
parser.add_argument('-o', '--fov', type=str,
required=False, help='List of fields of view to analyze. Input "1", "1,2,3", or "1-10", etc.')
# parser.add_argument('-p', '--peak', type=str,
# required=False, help='List of peak ids to analyze. Input "1", "1,2,3", or "1-10", etc.')
parser.add_argument('-j', '--nproc', type=int,
required=False, help='Number of processors to use.')
parser.add_argument('-m', '--modelfile', type=str,
required=False, help='Path to trained model.')
namespace = parser.parse_args()
# Load the project parameters file
mm3.information('Loading experiment parameters.')
if namespace.paramfile:
param_file_path = namespace.paramfile
else:
mm3.warning('No param file specified. Using 100X template.')
param_file_path = 'yaml_templates/params_SJ110_100X.yaml'
p = mm3.init_mm3_helpers(param_file_path) # initialized the helper library
if namespace.fov:
if '-' in namespace.fov:
user_spec_fovs = range(int(namespace.fov.split("-")[0]),
int(namespace.fov.split("-")[1])+1)
else:
user_spec_fovs = [int(val) for val in namespace.fov.split(",")]
else:
user_spec_fovs = []
# set switches and parameters
parser = argparse.ArgumentParser(prog='python mm3_Compile.py',
description='Identifies and slices out channels into individual TIFF stacks through time.')
parser.add_argument('-f', '--paramfile', type=str,
required=True, help='Yaml file containing parameters.')
parser.add_argument('-o', '--fov', type=str,
required=False, help='List of fields of view to analyze. Input "1", "1,2,3", or "1-10", etc.')
parser.add_argument('-j', '--nproc', type=int,
required=False, help='Number of processors to use.')
parser.add_argument('-m', '--modelfile', type=str,
required=False, help='Path to trained U-net model.')
namespace = parser.parse_args()
# Load the project parameters file
mm3.information('Loading experiment parameters.')
if namespace.paramfile:
param_file_path = namespace.paramfile
else:
mm3.warning('No param file specified. Using 100X template.')
param_file_path = 'yaml_templates/params_SJ110_100X.yaml'
p = mm3.init_mm3_helpers(param_file_path) # initialized the helper library
if namespace.fov:
if '-' in namespace.fov:
user_spec_fovs = range(int(namespace.fov.split("-")[0]),
int(namespace.fov.split("-")[1])+1)
else:
user_spec_fovs = [int(val) for val in namespace.fov.split(",")]
else:
user_spec_fovs = []
'--fov',
type=str,
required=False,
help='List of fields of view to analyze. Input "1", "1,2,3", etc. ')
parser.add_argument(
'-c',
'--cellfile',
type=file,
required=False,
help=
'Path to Cell object dicionary to analyze. Defaults to complete_cells.pkl.'
)
namespace = parser.parse_args()
# Load the project parameters file
mm3.information('Loading experiment parameters.')
if namespace.paramfile.name:
param_file_path = namespace.paramfile.name
else:
mm3.warning('No param file specified. Using 100X template.')
param_file_path = 'yaml_templates/params_SJ110_100X.yaml'
p = mm3.init_mm3_helpers(param_file_path) # initialized the helper library
if namespace.fov:
user_spec_fovs = [int(val) for val in namespace.fov.split(",")]
else:
user_spec_fovs = []
# load cell file
mm3.information('Loading cell data.')
if namespace.cellfile:
'--paramfile',
type=str,
required=True,
help='Yaml file containing parameters.')
parser.add_argument(
'-o',
'--fov',
type=str,
required=False,
help=
'List of fields of view to analyze. Input "1", "1,2,3", or "1-3", etc.'
)
namespace = parser.parse_args()
# Load the project parameters file
mm3.information('Loading experiment parameters.')
if namespace.paramfile:
param_file_path = namespace.paramfile
else:
mm3.warning('No param file specified. Using 100X template.')
param_file_path = 'yaml_templates/params_SJ110_100X.yaml'
p = mm3.init_mm3_helpers(param_file_path) # initialized the helper library
if namespace.fov:
if '-' in namespace.fov:
user_spec_fovs = range(int(namespace.fov.split("-")[0]),
int(namespace.fov.split("-")[1]) + 1)
else:
user_spec_fovs = [int(val) for val in namespace.fov.split(",")]
else:
user_spec_fovs = []
parser = argparse.ArgumentParser(prog='python mm3_Segment.py',
description='Segment cells and create lineages.')
parser.add_argument('-f', '--paramfile', type=str,
required=True, help='Yaml file containing parameters.')
parser.add_argument('-i', '--infile', type=str,
required=False, help='Use this argument to segment ONLY on image. Name the single file to be segmented.')
parser.add_argument('-o', '--fov', type=str,
required=False, help='List of fields of view to analyze. Input "1", "1,2,3", or "1-10", etc.')
parser.add_argument('-j', '--nproc', type=int,
required=False, help='Number of processors to use.')
parser.add_argument('-m', '--modelfile', type=str,
required=False, help='Path to trained U-net model.')
namespace = parser.parse_args()
# Load the project parameters file
mm3.information('Loading experiment parameters.')
if namespace.paramfile:
param_file_path = namespace.paramfile
else:
mm3.warning('No param file specified. Using 100X template.')
param_file_path = 'yaml_templates/params_SJ110_100X.yaml'
p = mm3.init_mm3_helpers(param_file_path) # initialized the helper library
if namespace.fov:
if '-' in namespace.fov:
user_spec_fovs = range(int(namespace.fov.split("-")[0]),
int(namespace.fov.split("-")[1])+1)
else:
user_spec_fovs = [int(val) for val in namespace.fov.split(",")]
else:
user_spec_fovs = []
if __name__ == "__main__":
'''
This script adds foci location information onto an existing dictionary of cells.
'''
# set switches and parameters
parser = argparse.ArgumentParser(prog='python mm3_Foci.py',
description='Finds foci.')
parser.add_argument('-f', '--paramfile', type=str,
required=True, help='Yaml file containing parameters.')
parser.add_argument('-c', '--cellfile', type=str,
required=False, help='Path to Cell object dicionary to analyze. Defaults to complete_cells.pkl.')
namespace = parser.parse_args()
# Load the project parameters file
mm3.information('Loading experiment parameters.')
if namespace.paramfile:
param_file_path = namespace.paramfile
else:
mm3.warning('No param file specified. Using 100X template.')
param_file_path = 'yaml_templates/params_SJ110_100X.yaml'
p = mm3.init_mm3_helpers(param_file_path) # initialized the helper library
# load cell file
mm3.information('Loading cell data.')
if namespace.cellfile:
cell_file_path = namespace.cellfile
else:
mm3.warning('No cell file specified. Using complete_cells.pkl.')
cell_file_path = os.path.join(p['cell_dir'], 'complete_cells.pkl')
'-o',
'--fov',
type=str,
required=False,
help=
'List of fields of view to analyze. Input "1", "1,2,3", or "1-10", etc.'
)
parser.add_argument('-j',
'--nproc',
type=int,
required=False,
help='Number of processors to use.')
namespace = parser.parse_args()
# Load the project parameters file
mm3.information('Loading experiment parameters.')
if namespace.paramfile:
param_file_path = namespace.paramfile
else:
mm3.warning('No param file specified. Using 100X template.')
param_file_path = 'yaml_templates/params_SJ110_100X.yaml'
p = mm3.init_mm3_helpers(param_file_path) # initialized the helper library
if namespace.fov:
if '-' in namespace.fov:
user_spec_fovs = range(int(namespace.fov.split("-")[0]),
int(namespace.fov.split("-")[1]) + 1)
else:
user_spec_fovs = [int(val) for val in namespace.fov.split(",")]
else:
user_spec_fovs = []
def track_loop(fov_id,
peak_id,
params,
tracks,
model_dict,
cell_number=6,
phase_file_name=None,
seg_file_name=None):
if phase_file_name is None:
seg_stack = mm3.load_stack(fov_id, peak_id, color=params['seg_img'])
phase_stack = mm3.load_stack(fov_id,
peak_id,
color=params['phase_plane'])
else:
seg_stack = io.imread(seg_file_name)
phase_stack = io.imread(phase_file_name)
# run predictions for each tracking class
# consider only the top six cells for a given trap when doing tracking
frame_number = seg_stack.shape[0]
# sometimes a phase contrast image is missed and has no signal.
# This is a workaround for that problem
no_signal_frames = []
for k, img in enumerate(phase_stack):
# if the mean phase image signal is less than 200, add its index to list
if np.mean(img) < 200:
no_signal_frames.append(k)
# loop through segmentation stack and replace frame from missed phase image
# with the prior frame.
for k, label_img in enumerate(seg_stack):
if k in no_signal_frames:
seg_stack[k, ...] = seg_stack[k - 1, ...]
regions_by_time = [
measure.regionprops(label_image=img) for img in seg_stack
]
# have generator yield info for top six cells in all frames
prediction_generator = mm3.PredictTrackDataGenerator(
regions_by_time, batch_size=frame_number, dim=(cell_number, 5, 9))
cell_info = prediction_generator.__getitem__(0)
predictions_dict = {}
# run data through each classification model
for key, mod in model_dict.items():
# Run predictions and add to dictionary
if key in [
'zero_cell_model', 'one_cell_model', 'two_cell_model',
'geq_three_cell_model'
]:
continue
mm3.information(
'Predicting probability of {} events in FOV {}, trap {}.'.format(
'_'.join(key.split('_')[:-1]), fov_id, peak_id))
predictions_dict['{}_predictions'.format(key)] = mod.predict(cell_info)
G, graph_df = mm3.initialize_track_graph(
peak_id=peak_id,
fov_id=fov_id,
experiment_name=params['experiment_name'],
predictions_dict=predictions_dict,
regions_by_time=regions_by_time,
born_threshold=0.85,
appear_threshold=0.85)
tracks.update(mm3.create_lineages_from_graph(G, graph_df, fov_id, peak_id))
type=str,
required=False,
help='Path to trained born model.')
parser.add_argument('--specfile',
type=str,
required=False,
help='Path to specs file.')
parser.add_argument('--timefile',
type=str,
required=False,
help='Path to file containing time table.')
namespace = parser.parse_args()
# Load the project parameters file
mm3.information('Loading experiment parameters.')
if namespace.paramfile:
param_file_path = namespace.paramfile
else:
mm3.warning('No param file specified. Using 100X template.')
param_file_path = 'yaml_templates/params_SJ110_100X.yaml'
p = mm3.init_mm3_helpers(param_file_path) # initialized the helper library
if namespace.fov:
if '-' in namespace.fov:
user_spec_fovs = range(int(namespace.fov.split("-")[0]),
int(namespace.fov.split("-")[1]) + 1)
else:
user_spec_fovs = [int(val) for val in namespace.fov.split(",")]
else:
user_spec_fovs = []
parser = argparse.ArgumentParser(prog='python mm3_TrackFoci.py',
description='Track fluorescent foci.')
parser.add_argument('-f', '--paramfile', type=str,
required=True, help='Yaml file containing parameters.')
parser.add_argument('-o', '--fov', type=str,
required=False, help='List of fields of view to analyze. Input "1", "1,2,3", or "1-10", etc.')
parser.add_argument('-j', '--nproc', type=int,
required=False, help='Number of processors to use.')
parser.add_argument('-c', '--channel', type=int,
required=False, default=2,
help='Which channel, as an integer, contains your fluorescent foci data? \
Accepts integers. Default is 2.')
namespace = parser.parse_args()
# Load the project parameters file
mm3.information('Loading experiment parameters.')
if namespace.paramfile:
param_file_path = namespace.paramfile
else:
mm3.warning('No param file specified. Using 100X template.')
param_file_path = 'yaml_templates/params_SJ110_100X.yaml'
p = mm3.init_mm3_helpers(param_file_path) # initialized the helper library
if namespace.fov:
if '-' in namespace.fov:
user_spec_fovs = range(int(namespace.fov.split("-")[0]),
int(namespace.fov.split("-")[1])+1)
else:
user_spec_fovs = [int(val) for val in namespace.fov.split(",")]
else:
user_spec_fovs = []
# set switches and parameters
parser = argparse.ArgumentParser(
prog='python combine_tracks_from_chtc.py',
description=
'CHTC saves a separate track file for each fov/peak. Here we combine them.'
)
parser.add_argument('-f',
'--paramfile',
type=str,
required=True,
help='Yaml file containing parameters.')
namespace = parser.parse_args()
# Load the project parameters file
mm3.information('Loading experiment parameters.')
if namespace.paramfile:
param_file_path = namespace.paramfile
else:
mm3.warning('No param file specified. Using 100X template.')
param_file_path = 'yaml_templates/params_SJ110_100X.yaml'
p = mm3.init_mm3_helpers(param_file_path) # initialized the helper library
# Get file names
fnames = glob.glob(
os.path.join(p['cell_dir'],
"{}*_tracks.pkl".format(p['experiment_name'])))
### Now prune and save the data.
mm3.information("Reading cell data from each file and combining into one.")
# set switches and parameters
parser = argparse.ArgumentParser(prog='python mm3_Segment.py',
description='Segment cells and create lineages.')
parser.add_argument('-f', '--paramfile', type=str,
required=True, help='Yaml file containing parameters.')
parser.add_argument('-o', '--fov', type=str,
required=False, help='List of fields of view to analyze. Input "1", "1,2,3", or "1-10", etc.')
parser.add_argument('-j', '--nproc', type=int,
required=False, help='Number of processors to use.')
parser.add_argument('-s', '--segmentsource', type=str,
required=False, help='Segmented images to use for tracking. "seg_otsu", "seg_unet", etc.')
namespace = parser.parse_args()
# Load the project parameters file
mm3.information('Loading experiment parameters.')
if namespace.paramfile:
param_file_path = namespace.paramfile
else:
mm3.warning('No param file specified. Using 100X template.')
param_file_path = 'yaml_templates/params_SJ110_100X.yaml'
p = mm3.init_mm3_helpers(param_file_path) # initialized the helper library
if namespace.fov:
if '-' in namespace.fov:
user_spec_fovs = range(int(namespace.fov.split("-")[0]),
int(namespace.fov.split("-")[1])+1)
else:
user_spec_fovs = [int(val) for val in namespace.fov.split(",")]
else:
user_spec_fovs = []