Time-Lapse TIFF Viewer

A PyQt5-based application for viewing and analyzing time-lapse TIFF images, specifically designed for inspecting single nucleus time-lapse data with RNA track visualization and saving capabilities.

Features

• Load and display time-lapse TIFF images from specified directories.
• Scroll through frames using a slider to inspect tracking quality.
• Visualize RNA tracks with customizable overlays (yellow circles and labels).
• Select and save specific tracks and frame ranges to an output directory.
• Support for navigating multiple time-stack files.
• Maintains folder structure for saved files (e.g., annotated/unannotated images, spot intensity tables).

Prerequisites

• Python 3.8 or higher
• Required Python packages:

  pip install PyQt5 tifffile numpy pandas Pillow scikit-image opencv-python
  

Installation

Clone this repository:

git clone https://github.com/CBIIT/ImageViewer.git
cd ImageViewer

Install the required dependencies (see Prerequisites).

Usage

Run the application:

python ImageViewer.py

This launches the Time-Lapse TIFF Viewer GUI.

Load Time-Lapse TIFF

• Click the "Load Time-Lapse TIFF" button.
• Select TIFF files from either the /cell_tracking/spot_image_patches or /cell_tracking/annotated_spot_image_patches directory.
• The first single nucleus time-lapse will be displayed.

Select Output Folder

• Click the "Select Output Folder" button to specify where to save inspected or modified tracks.
• Output will maintain the same subfolder structure as the source cell_tracking folder.

Inspect the Time-Lapse

• Use the scroll bar below the image to navigate through the time-lapse frames and verify tracking quality.
• RNA tracks are displayed with yellow circles and labels on the image.

Manage Tracks

• On the right panel, toggle checkboxes to include or exclude specific RNA tracks (e.g., to remove mis-segmented burst tracks).
• Adjust the minimum and maximum frame numbers using the spin boxes on the bottom right to select a specific frame range.

Save Current Time-Stack

• If the tracking is satisfactory, click "Save Current Time-Stack".
• Saves the current image, selected tracks, and related files (e.g., spot intensity tables, nuclei images) to the output folder.
• If a frame range is specified, only the selected frames are saved.

Load Next Time-Stack

• Click "Next Time-Stack" to load the next single nucleus time-lapse for inspection.
• Repeat the process until all images are inspected.

File Structure

The application expects and generates files in the following structure:

cell_tracking/
├── annotated_spot_image_patches/
├── spot_image_patches/
├── unannotated_spot_image_patches/
├── spot_intensity_tables/
│   ├── complete_tables/
│   └── integrated_intensity_tables/
├── single_track_images/
└── single_track_tables/

• Input: TIFF files must be loaded from spot_image_patches or annotated_spot_image_patches.
• Output: Saved files are organized into the same subfolder structure in the user-specified output directory.

Notes

• Ensure the input TIFF files follow the naming convention:
  • colX_rowY_fieldZ_cellW_ChV.tif (e.g., col1_row2_field3_cell4_Ch5.tif).
• Spot intensity tables should be in CSV or TRK format with appropriate column names:
  • e.g., chV_spot_no_W_x, chV_spot_no_W_y
• The application handles multiple channels and copies unannotated images for other channels when saving.

Contributing

Contributions are welcome! Please submit a pull request or open an issue for bugs, feature requests, or improvements.

License

This project is licensed under the MIT License. See the LICENSE file for details.

Acknowledgments

• Developed for analyzing single nucleus time-lapse data in a research context.