Metadata-Version: 2.1
Name: rsnaped
Version: 0.0.1
Summary: Python module for single-molecule image processing.
Home-page: https://github.com/MunskyGroup/rsnaped
Author: Luis Aguilera
Author-email: luisubald@gmail.com
License: MIT
Description: # rSNAPed
        [![License: MIT](https://img.shields.io/badge/License-MIT-yellow.svg)](https://opensource.org/licenses/MIT)
        
        rSNAPed a Python library for single-molecule image processing.
        
        Author Luis U. Aguilera
        
        ## Description
        
        ## Automated Single-molecule tracking
        
        The code is intended to automatically track single-molecules from single-cell videos. The code calculates spot position and extract intensity values.
        
        Compendium of libraries including `cellpose`, `rsnapsim`, `trackpy`.
        
        ![Screenshot](https://github.com/MunskyGroup/image_processing_toolbox/blob/master/rSNAPsim_IP/General_Documents/Images_for_github/rSNAPsimIP_Pipeline.png)
        
        
        ## Usage
        
        
        
        * **Single-molecule translation**
        * **Single-molecule transcription**
        * **FISH**
        
        Example using real data.
        
        ![Screenshot](https://github.com/MunskyGroup/image_processing_toolbox/blob/master/rSNAPsim_IP/General_Documents/Images_for_github/screenshot_3.png)
        
        ## Simulating translation
        
        The code is intended to simulated single-
        molecule translation. A  video with the simulated cell and a data frame containing spot and intensity positions are generated. This simulation can be used to train new algorithms or for training new students.
        
        ![Screenshot](https://github.com/MunskyGroup/image_processing_toolbox/blob/master/rSNAPsim_IP/Simulated_Cell/Development/Gifs/output.gif)
        
        ## Installation
        
        First make sure that you have installed the following packages. For this, you can use the package manager [pip](https://pip.pypa.io/en/stable/).
        
        ## The codes were tested with the following packages.
        
        matplotlib (3.2.2) <br />
        numpy (1.20.1) <br />
        pandas (1.0.5) <br />
        scikit-image (0.18.0) <br />
        joblib (0.16.0) <br />
        bqplot (0.12.17) <br />
        scipy (1.5.0) <br />
        cellpose (0.5.1) <br />
        pyfiglet (0.8.post1) <br />
        tifffile (2020.10.1) <br />
        opencv-python (4.4.0.42) <br />
        trackpy (0.4.2) <br />
        ipywidgets (7.5.1) <br />
        
        ## To install all packages please open installation.ipynb and run the notebook.
        ![Screenshot](https://github.com/MunskyGroup/image_processing_toolbox/blob/master/rSNAPsim_IP/General_Documents/Images_for_github/screenshot_4.png)
        
        
        ## If you want to manually install the dependencies run the following lines on the terminal
        
        ```bash
        pip3 install scikit-image
        pip3 install ipywidgets
        pip3 install bqplot
        pip3 install scipy
        pip3 install pyfiglet
        pip3 install opencv-python
        pip3 install cellpose
        pip3 install trackpy
        pip3 install ipywidgets
        ```
        
        ## If cellpose installation doesn't work, try the following:
        ```bash
        pip3 install --no-deps cellpose --upgrade
        pip3 install mxnet
        pip3 install natsort
        ```
        
        ## Use the following commands to update specific packages:
        ```bash
        !pip3 install '[package_name]==[version]'
        !pip3 install [package_name] -U
        !pip3 show [package_name]
        ```
        
        
        ## License
        [MIT](https://choosealicense.com/licenses/mit/)
        
Keywords: single-molecule image processing
Platform: UNKNOWN
Classifier: Development Status :: 2 - Pre-Alpha
Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
Classifier: Topic :: Scientific/Engineering :: Image Processing
Classifier: License :: OSI Approved :: MIT License
Classifier: Programming Language :: Python :: 3.8
Requires-Python: >=3.7
Description-Content-Type: text/markdown
