GridFree: A pixel-level label tools to segment high-throughput images

Article link: https://academic.oup.com/plphys/advance-article/doi/10.1093/plphys/kiab226/6274909

Bibtex @article{10.1093/plphys/kiab226, author = {Hu, Yang and Zhang, Zhiwu}, title = "{GridFree: A Python Package of Image Analysis for Interactive Grain Counting and Measuring}", journal = {Plant Physiology}, year = {2021}, month = {05}, issn = {0032-0889}, doi = {10.1093/plphys/kiab226}, url = {https://doi.org/10.1093/plphys/kiab226}, note = {kiab226}, eprint = {https://academic.oup.com/plphys/advance-article-pdf/doi/10.1093/plphys/kiab226/37929045/kiab226.pdf}, }

Implement Python version 3.6.5(Windows 10 64bit version is available, check the download link below)

install Python 3.6.5, download link: https://www.python.org/downloads/release/python-365/

MacOS

install

execute python3.6 -m pip install -r requirements.txt to install required packages

run the software

execute ./run on a terminal to run the software

Linux OS

install

execute python3.6 -m pip install -r requirements.txt to install required packages

run the software

execute ./run on a terminal to run the software

Windows OS

Windows 10 64bit (Download and run `tkinterGUI_nw.exe` in dist folder)

Download link: https://www.dropbox.com/s/nf6vsu1q5meb1ho/GridFree_winOS.zip?dl=0

install (if Windows 10 64bit doesn't work for you)

run cmd go to the path you downloaded GridFree, you can execute cd space your download path
execute python -m pip install -r requirements.txt to install required packages
execute python -m pip install opencv-python for opencv package
execute python -m pip install scikit-image for package installation
execute python -m pip install sklearn for package installation
YouTube: https://youtu.be/fSgH1-35Hyw

run the software

execute python tkinterGUI_nw.py to run the software

If crashed

Modify matplotlibrc file ADD: backend: TkAgg

Name		Name	Last commit message	Last commit date
Latest commit History 306 Commits
.github/ISSUE_TEMPLATE		.github/ISSUE_TEMPLATE
SampleImages		SampleImages
wikiimgs		wikiimgs
480demo.gif		480demo.gif
GridFree_GUI.py		GridFree_GUI.py
LICENSE		LICENSE
PolygonSelectionDemo.gif		PolygonSelectionDemo.gif
PolygonSelectionDemo.mov		PolygonSelectionDemo.mov
README.md		README.md
__init__.py		__init__.py
annotate.txt		annotate.txt
areasel_gridfree.gif		areasel_gridfree.gif
areaselection.gif		areaselection.gif
axistest.py		axistest.py
batchprocess.py		batchprocess.py
batchprocess_terminal.py		batchprocess_terminal.py
bottom_frame.py		bottom_frame.py
cal_kernelsize.py		cal_kernelsize.py
calculator.py		calculator.py
cmb10.ttf		cmb10.ttf
colorindicestest.py		colorindicestest.py
colorstripgen.py		colorstripgen.py
compare.png		compare.png
config.pickle		config.pickle
control_frame.py		control_frame.py
corns_demo.gif		corns_demo.gif
countlist.csv		countlist.csv
createBins.py		createBins.py
crop.png		crop.png
cropimg_extraction.py		cropimg_extraction.py
defines		defines
displaypanel.py		displaypanel.py
distributionplot.R		distributionplot.R
filterpanel.py		filterpanel.py
guicontainer.py		guicontainer.py
histograms.py		histograms.py
kplus.py		kplus.py
lm_method.py		lm_method.py
mainfunctions.py		mainfunctions.py
normaldistribution.png		normaldistribution.png
origins.py		origins.py
processimgs.py		processimgs.py
rasterio-1.0.24+gdal24-cp36-cp36m-win32.whl		rasterio-1.0.24+gdal24-cp36-cp36m-win32.whl
rasterio-1.0.24+gdal24-cp36-cp36m-win_amd64.whl		rasterio-1.0.24+gdal24-cp36-cp36m-win_amd64.whl
requirements.txt		requirements.txt
run		run
run_oldmac		run_oldmac
sampleseed-demo.gif		sampleseed-demo.gif
seed.png		seed.png
seedsample.JPG		seedsample.JPG
sel_area.py		sel_area.py
sensordata.py		sensordata.py
showtip.py		showtip.py
testbandimages.py		testbandimages.py
testmagnifier.py		testmagnifier.py
testtkinterplot.py		testtkinterplot.py
tkinterGUI.py		tkinterGUI.py
tkinterGUI_nw.py		tkinterGUI_nw.py
tkintercore.py		tkintercore.py
tkintercorestat.py		tkintercorestat.py
tkintercorestat_plot.py		tkintercorestat_plot.py
tkintersinglecore.py		tkintersinglecore.py
trainingdataset.csv		trainingdataset.csv
trainmodel.py		trainmodel.py
wheatdemo.gif		wheatdemo.gif
win-smallw-startdemo.gif		win-smallw-startdemo.gif
zoomtest.py		zoomtest.py

License

12HuYang/GridFree

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GridFree: A pixel-level label tools to segment high-throughput images

Article link: https://academic.oup.com/plphys/advance-article/doi/10.1093/plphys/kiab226/6274909

Implement Python version 3.6.5(Windows 10 64bit version is available, check the download link below)

MacOS

install