Commit 1724ee10 authored by Christoph Sommer's avatar Christoph Sommer
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Merge branch 'csommer-master-patch-42604' into 'master'

Update README.md

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# 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
in [Radler et al.](https://www.biorxiv.org/content/10.1101/2021.11.08.467681v1.article-info)
FRAPdiff is based on a [fitting routine](https://github.com/davidmrutkowski/1DReflectingDiffusion) developed and kindly shared by David Rutkowski and colleagues.
## Example
......@@ -9,11 +12,8 @@ in Gerganova et al. https://www.biorxiv.org/content/10.1101/2020.12.18.423457v3
Open a (Anaconda) command-line shell and type.
`frapdiff`
### 2. Command-line interface
Open a command-line shell and type.
`frapdiff -h`
### 3. Jupyter notebook
### 2. Jupyter notebook
```python
from frapdiff import frapdiff
......@@ -32,6 +32,55 @@ result_dict = frapdiff.extract_frap_profiles_and_fit(
)
```
### 3. Command-line interface
Open a command-line shell and type.
`frapdiff -h`
This will show the command line usage and all
```
usage: frapdiff [-h] -d INPUT_DIR [-r] -o OUTPUT [-b] [-bs CORRECTION_REGION_SIZE] [-p {vertical,horizontal}]
[-e EXTEND] [-m {No,first_half,second_half}] [-D D_INITIAL] [-K KOFF_INITIAL] [-min_lf MINIMUM_LF]
[-max_lf MAXIMUM_LF]
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 [Radler et al.](https://www.biorxiv.org/content/10.1101/2021.11.08.467681v1.article-info)
optional arguments:
-h, --help show this help message and exit
General:
-d INPUT_DIR, --input_dir INPUT_DIR
Input Folder containing movies (.tif)
-r, --recursive Search movies in input folder recursively
-o OUTPUT, --output OUTPUT
Output file (.tab)
Bleach correction:
-b, --bleach_correction
Perfom simple, ratio-based bleach correction in upper-left window
-bs CORRECTION_REGION_SIZE, --correction_region_size CORRECTION_REGION_SIZE
Size of bleach-correction window (upper left corner)
FRAP region:
-p {vertical,horizontal}, --project_values {vertical,horizontal}
-e EXTEND, --extend EXTEND
Extend original FRAP window by this factor to both sides each.
-m {No,first_half,second_half}, --mirror_values {No,first_half,second_half}
Mirror intensity values. Use, when original profiles are not symmetric.
Fitting:
-D D_INITIAL, --D_initial D_INITIAL
Initial guess for diffusion
-K KOFF_INITIAL, --Koff_initial KOFF_INITIAL
Initial guess for K_off
-min_lf MINIMUM_LF, --minimum_Lf MINIMUM_LF
Minimum L_f to restrict solver to reasonable values
-max_lf MAXIMUM_LF, --maximum_Lf MAXIMUM_LF
Maximum L_f to restrict solver to reasonable values
```
## Installation
### pip (developer, recommended)
1. Clone this repository
......@@ -45,3 +94,4 @@ result_dict = frapdiff.extract_frap_profiles_and_fit(
numpy, pandas, tifffile, roifile, Gooey, wxPython, scipy, matplotlib
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