rsnaped 0.0.1

Python module for single-molecule image processing.

rSNAPed

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.

Usage

• Single-molecule translation
• Single-molecule transcription
• FISH

Example using real data.

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.

Installation

First make sure that you have installed the following packages. For this, you can use the package manager pip.

The codes were tested with the following packages.

matplotlib (3.2.2)
numpy (1.20.1)
pandas (1.0.5)
scikit-image (0.18.0)
joblib (0.16.0)
bqplot (0.12.17)
scipy (1.5.0)
cellpose (0.5.1)
pyfiglet (0.8.post1)
tifffile (2020.10.1)
opencv-python (4.4.0.42)
trackpy (0.4.2)
ipywidgets (7.5.1)

To install all packages please open installation.ipynb and run the notebook.

If you want to manually install the dependencies run the following lines on the terminal

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:

pip3 install --no-deps cellpose --upgrade
pip3 install mxnet
pip3 install natsort

Use the following commands to update specific packages:

!pip3 install '[package_name]==[version]'
!pip3 install [package_name] -U
!pip3 show [package_name]

License

MIT