MicroscopyAnalysis_Tutorial

This repository is used to showcase the basic usage of automated microscopy image analysis The automated iamge analysis pipeline include:

Image preprocessing
Vesicle detection
Batch processing

Installation

Follow these steps to set up the Microscopy Analysis Tutorial on your computer:

Step 1: Install Python

Option 1:

If you don't have Anaconda installed, download and install it from anaconda.com. Anaconda includes Python and Jupyter Notebook.

Option 2:

If you don't have Python installed, download and install it from python.org. Make sure to check the option to add Python to your PATH during installation.

We recommend to install Anaconda for non-coding experience user.

Step 2: Download the Project Files

Go to the GitHub repository.
Click the green "Code" button and select "Download ZIP".
Extract the downloaded ZIP file to a folder on your computer.

Step 3: Install Dependencies

Option 1: install dependencies from Anaconda

User should only need to install these packages: matplotlib numpy pandas scikit-image opencv-python Open Anaconda, search the pacakges in 'Not installed' menu, check the packages and click apply.

Option 2: install dependencies from terminal

Open a command prompt (Windows) or terminal (macOS/Linux).
Navigate to the folder where you extracted the project files. For example:
```
cd path/to/MicroscopyAnalysis_Tutorial
```
Install the required Python packages by running:
```
pip install matplotlib numpy pandas scikit-image opencv-python
```
User should only need to install the above packages, if you need to know the full environment dependencies, you can check it in MicroscopyAnalysis/requirements.txt.

Step 4: Run the scripts

Run the main script in jupyter notebook. Copy the code in the Usage section(Next section) and run.
Run the main script in terminal, use the following command in your terminal:

python main.py <file_folder> <PlateName> [--templates <template_file1> <template_file2> ... <template_fileN>]

Examples:

Using Default Templates:

python main.py Data/Test_0517 Plate_2024605

Using Custom Templates:

python main.py Data/Test_0517 Plate_2024605 --templates Templates/custom_template1.npy Templates/custom_template2.npy

Usage

This section show the minimal code examples illustrating how to use the functions. You can also check the documentation site.

Here we provide some example code to analysis batch images from a folder. Three parameters are needed for main function. file_folder: The folder stored the images that needed to be analyzed templates: A list of templates files PlateName: Used for saving results

import os
import time
import numpy as np

from MicroscopyAnalysis.batch_run import run_batch_files_templates
from MicroscopyAnalysis.main import main

# Adjust paths to the templates
template1 = np.load(os.path.join('Templates', 'template_656, 640, 71, 71.npy'))
template2 = np.load(os.path.join('Templates', 'Project_Whole Plate1_1024x1024_200Hz_1%Laser_800gain_B_5_R1.tif_enhance_482_20_56_56.npy'))
template3 = np.load(os.path.join('Templates', '1024x1024 - 4 point_no-z-stack - split 5 rows rows only_TileScan 1_C_11_R2.npy'))
templates = [template1, template2, template3]

# Adjust the path to the data folder
file_folder = os.path.join('Data', 'Test_0517')
PlateName = 'Plate_2024605'

# Example usage
main(file_folder, templates, PlateName)

License

Distributed under the Apache License 2.0. See the LICENSE file for more information.

Contact

Academic collaborations and extensions/improvements by the community are encouraged. Please contact HL by email if you have questions.

Citations

TBD

hliu56/MicroscopyAnalysis_Tutorial