Commit 4e187729 authored by Christoph Sommer's avatar Christoph Sommer
Browse files

more doc

parent d3cc4638
# FRAPdiff
FRAP analysis on .tif movies containing an ImageJ ROI of the bleach rectangle.
FRAPdiff estimates K_off and diffusion. Detail are described in further detail
in Gerganova et al. https://www.biorxiv.org/content/10.1101/2020.12.18.423457v3
## Example
......@@ -8,8 +11,6 @@
#### Dependencies
* numpy
* pandas
* networkx
numpy, pandas, tifffile, roifile, Gooey, wxPython
......@@ -200,7 +200,13 @@ def main_cli():
"""
parser = GooeyParser()
parser = GooeyParser(
description="""FRAP analysis on .tif movies containing an ImageJ ROI
of the bleach rectangle. FRAPdiff estimates K_off and
Diffusion parameters. Detail are described in further
detail in Gerganova et al. https://www.biorxiv.org/content/10.1101/2020.12.18.423457v3
"""
)
in_movies_parser = parser.add_argument_group("General")
in_movies_parser.add_argument(
......@@ -216,7 +222,7 @@ def main_cli():
"--recursive",
action="store_true",
gooey_options={"initial_value": True},
help="Seach movies in input folder recursively",
help="Search movies in input folder recursively",
)
in_movies_parser.add_argument(
......@@ -238,7 +244,7 @@ def main_cli():
"--bleach_correction",
action="store_true",
gooey_options={"initial_value": True},
help="Perfom simple ratio-based bleach correction",
help="Perfom simple, ratio-based bleach correction in upper-left window",
)
bleach_corr_parser.add_argument(
......@@ -246,7 +252,7 @@ def main_cli():
"--correction_region_size",
widget="IntegerField",
gooey_options={"min": 0, "max": 999, "increment": 1, "initial_value": 150},
help="Size of bleach-correction region (upper left corner)",
help="Size of bleach-correction window (upper left corner)",
type=int,
)
......@@ -266,7 +272,7 @@ def main_cli():
"--extend",
widget="DecimalField",
gooey_options={"min": 0, "max": 3.0, "increment": 0.1, "initial_value": 1.5},
help="Extend original FRAP window to both sides",
help="Extend original FRAP window by this factor to both sides each.",
type=float,
)
......@@ -275,7 +281,7 @@ def main_cli():
"--mirror_values",
widget="Dropdown",
choices=["No", "first_half", "second_half"],
help="Mirror values",
help="Mirror intensity values. Use, when original profiles are not symmetric.",
gooey_options={"initial_value": "first_half"},
type=str,
)
......@@ -296,7 +302,7 @@ def main_cli():
"--Koff_initial",
widget="DecimalField",
gooey_options={"min": 0, "max": 3.0, "increment": 0.01, "initial_value": 0.1},
help="Initial guess for Koff",
help="Initial guess for K_off",
type=float,
)
......@@ -305,7 +311,7 @@ def main_cli():
"--minimum_Lf",
widget="DecimalField",
gooey_options={"min": 0, "max": 20.0, "increment": 1.0, "initial_value": 8},
help="Minimum Lf",
help="Minimum L_f to restrict solver to reasonable values",
type=float,
)
......@@ -314,7 +320,7 @@ def main_cli():
"--maximum_Lf",
widget="DecimalField",
gooey_options={"min": 0, "max": 20.0, "increment": 1.0, "initial_value": 16},
help="Maximum Lf",
help="Maximum L_f to restrict solver to reasonable values",
type=float,
)
......@@ -331,7 +337,7 @@ def main_cli():
results = []
n = len(all_mov_fns)
for i, mov_fn in enumerate(all_mov_fns):
print(f"# {i+1}/{n} ### {mov_fn}")
print(f"\n# {i+1}/{n} ### {mov_fn}")
sys.stdout.flush()
try:
result_dict = extract_frap_profiles_and_fit(
......
Supports Markdown
0% or .
You are about to add 0 people to the discussion. Proceed with caution.
Finish editing this message first!
Please register or to comment