12huyang / gridfree

An App counts the number of components in an image.

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

Polygon Area selection segment demo

Area selection on PC and Cluster views

Area selection segment and delet demo

YouTube: https://youtu.be/oGYw1ZBcrhk

Wheat segment demo

YouTube: https://youtu.be/IxMBTT4fzr4

Chickpea segment demo

YouTube: https://youtu.be/be12xOfF614

Corns segment demo

YouTube: https://youtu.be/1ngHQsUFWH4

gridfree's Issues

Issues with windows version

Describe the bug
When I click segment on the windows app, it does not complete and so the program doesnt advance.

To Reproduce
Steps to reproduce the behavior:

1. upload image
2. select clusters
3. click eSgment
4. See error

Expected behavior
I would see the selected data for grain size

Screenshots
If applicable, add screenshots to help explain your problem.

Desktop (please complete the following information):

• OS: Windows 10

Additional context
This program looks great and I would love to use it. Let me know if you need anymore information.

Error has happen in run the program

see error
A clear and concise description of what the bug is.

while final step after installing all packages when try to run the command given by you it shows the following error

ImportError: cannot import name 'watershed' from 'skimage.morphology' (C:\Users\Tk\anaconda3\lib\site-packages\skimage\morphology_init_.py)

Additional context

so i unable to open the program