Merge branch 'master' of https://github.com/biswajitSM/LEADS into master

Author: romanbarth

README.md

@@ -34,15 +34,28 @@ And then install the leads program
 python setup.py install
 ```
 
-To save videos, install [ffmpeg](https://ffmpeg.org/download.html) and make sure you added it to your path (you can follow this [link](https://www.wikihow.com/Install-FFmpeg-on-Windows))
-
 ## Usage
 
-To open the gui of kymograph analysis from a terminal
-> python -m leads.gui.kymograph_gui
+### From a terminal or command prompt
 
-To open the gui for cropping large files in a folder
-> python -m leads.gui.crop_images_gui
+Activate environment in a terminal
+```sh
+conda activate leads-env
+```
+
+To open the gui of kymograph analysis
+```sh
+python -m leads.gui.kymograph_gui
+```
+
+To open the gui for cropping large number of image files in a folder
+```sh
+python -m leads.gui.crop_images_gui
+```
+
+### Alternative
+
+If you are in windows os, you can double click the bat script files [LEADS_kymoGUI.bat](./bat/LEADS_kymoGUI.bat) for the kymo program and [LEADS_cropGUI.bat](./bat/LEADS_cropGUI.bat) for the cropping program.
 
 ## Contributing
 
@@ -56,3 +69,13 @@ List of contributors:
 
 - Biswajit Pradhan (biswajitp145_at_gmail.com)
 - Roman Barth
+
+## Pubslihed articles based on this module
+
+[Condensin-driven loop extrusion on supercoiled DNA. *nature structural molecular biology*, 2022 (accepted)](https://doi.org/10.1101/2021.05.15.444164)
+
+[ParS-independent recruitment of the bacterial chromosome-partitioning protein ParB. *Science Advances*, 2022 (accepted)](https://doi.org/10.1101/2021.11.02.466941)
+
+[SMC complexes can traverse physical roadblocks bigger than their ring size, *bioRxiv*, 2021 (in press)](https://doi.org/10.1101/2021.07.15.452501)
+
+[The Smc5/6 complex is a DNA loop extruding motor. *bioRxiv*, 2022](https://doi.org/10.1101/2022.05.13.491800)

requirements.txt

@@ -3,21 +3,35 @@ numba
 pandas
 scipy
 scikit-image
-matplotlib==3.4.1
-PyQt5
-napari==0.4.8
+matplotlib
+napari
 pyqtgraph
 opencv-python
 dask
 pims
 trackpy
 tqdm
-tifffile==2020.6.3
-roifile==2020.5.28
-PyYAML==5.4.1
+tifffile
+roifile
+PyYAML
 h5py
 tables
 qdarkstyle
 colorharmonies
 XlsxWriter
-ptvsd
+ptvsd
+
+napari-simpleitk-image-processing
+napari-plot-profile
+napari-roi
+napari-plot
+napari-time-series-plotter
+napari-curtain
+# napari-nd-cropper
+napari-itk-io
+napari-features
+napari-elementary-numpy-operations
+napari-brightness-contrast
+napari-bil-data-viewer
+napari-animation
+napari-script-editor

setup.py

@@ -19,28 +19,28 @@
     ],
     python_requires = '>=3.7',
     install_requires = [
-        "numpy",
-        "numba",
-        "pandas",
-        "scipy",
-        "scikit-image",
-        "matplotlib==3.4.1",
-        "PyQt5",
-        "napari==0.4.8",
-        "pyqtgraph",
-        "opencv-python",
-        "dask",
-        "pims",
-        "trackpy",
-        "tqdm",
-        "tifffile==2020.6.3",
-        "roifile==2020.5.28",
-        "PyYAML",
-        "h5py",
-        "tables",
-        "qdarkstyle",
-        "colorharmonies",
-        "XlsxWriter"
+        # "numpy",
+        # "numba",
+        # "pandas",
+        # "scipy",
+        # "scikit-image",
+        # "matplotlib==3.4.1",
+        # "PyQt5",
+        # "napari==0.4.8",
+        # "pyqtgraph",
+        # "opencv-python",
+        # "dask",
+        # "pims",
+        # "trackpy",
+        # "tqdm",
+        # "tifffile==2020.6.3",
+        # "roifile==2020.5.28",
+        # "PyYAML",
+        # "h5py",
+        # "tables",
+        # "qdarkstyle",
+        # "colorharmonies",
+        # "XlsxWriter"
     ],
     dependency_links = ["git+https://github.com/pyqtgraph/pyqtgraph@master"]
 )