Filospot

A napari plugin for automating the loading, navigation, alignment, filter and export of image and spot data.

Installation

You can install filospot via pip:

pip install filospot

To install latest development version:

pip install git+https://github.com/qin-yu/filospot.git

Or install from source:

git clone https://github.com/qin-yu/filospot.git
cd filospot
pip install -e .

Usage

As a napari plugin

After installation, the plugin will be available in napari. You can access the filospot widget through:

• Plugins > filospot > Filospot - Image and Spot Analysis

The plugin provides a unified interface with sections for:

• Import: Load directories containing raw images, reference images, and CSV spot detection files
• Navigation: Browse through image datasets with Previous/Next buttons and dropdown selection
• Align Reference: Apply pixel-level translation to align reference images with main images
• Filtering: Filter detected spots based on intensity thresholds in reference images
• Export: Export filtered spots to CSV format

As a standalone application

filospot

This launches the full napari application with filospot widgets pre-loaded.

Programmatically

from filospot import main
main()

Or use individual components:

from filospot import DataNavigator, filter_spots_by_reference
from filospot.alignment import apply_pixel_translation

# Create a data navigator
navigator = DataNavigator()
navigator.load_paths(tif_dir, ref_dir, csv_dir)

# Apply image alignment
aligned_image = apply_pixel_translation(image, 0, 5, -2)

Features

• Multi-format support: Load TIFF images and CSV spot detection files
• Reference alignment: Pixel-level translation alignment with visual feedback
• Advanced filtering: Filter spots by intensity with optional Gaussian blur
• Live visualization: Real-time contrast updates and threshold visualization
• Batch processing: Navigate through entire datasets efficiently
• Export functionality: Save filtered results to CSV

Project Structure

• filospot/app.py - Main application entry point
• filospot/_widget.py - Napari plugin widget interface
• filospot/data_navigator.py - Data loading and navigation functionality
• filospot/alignment.py - Image alignment utilities
• filospot/filtering.py - Spot filtering functionality
• filospot/widgets.py - GUI widgets and interface components
• filospot/config.py - Configuration and constants
• filospot/napari.yaml - Napari plugin manifest
• tests/ - Test suite for plugin functionality
• conda-recipe/ - Conda package recipe for conda-forge distribution

Requirements

• Python >= 3.8
• napari[all]
• numpy
• pandas
• tifffile
• magicgui
• scipy