web_microview

A web-based microscope image viewer built with Bokeh for interactive visualization of TIFF microscopy data.

Overview

Languages: Python

Documentation

Web Microview

A web-based microscope image viewer built with Bokeh for interactive visualization of TIFF microscopy data.

Overview

Web Microview is an interactive dashboard for visualizing and analyzing microscopy images. It provides a user-friendly interface for viewing TIFF files, navigating through image stacks, adjusting contrast, and performing basic region-of-interest (ROI) analysis.

Features

TIFF File Support: Load and view single images or multi-frame TIFF stacks
Interactive Visualization: Pan, zoom, and navigate through image stacks
ROI Analysis: Select regions of interest and view detailed statistics
Image Enhancement: Adjust contrast with interactive controls
Metadata Viewer: Examine TIFF metadata in an organized display
Intensity Profiling: Visualize intensity profiles across the image (coming soon)

Installation

Prerequisites

Python 3.7+
pip

Setup

Clone the repository

git clone https://github.com/username/web_microview.git
cd web_microview

Create and activate a virtual environment (recommended)

python -m venv venv

# On Windows
venv\Scripts\activate

# On macOS/Linux
source venv/bin/activate

Install the required packages
```
pip install bokeh tifffile numpy scipy
```

Usage

Running the Application

Start the Bokeh server:
```
bokeh serve --show app.py
```
The application will open in your default web browser at http://localhost:5006/app

Using the Interface

Loading Images

Click the "Choose File" button and select a TIFF file (.tif or .tiff)
The image will automatically load and display in the main view

Navigating Image Stacks

Use the "Frame" slider to move through different frames in a multi-frame TIFF stack
The slider will only appear when a multi-frame image is loaded

Adjusting

[View full README on GitHub]