Lattice Light-Sheet Microscopy Datasets and Workflow for Omero

Dataset Overview

This dataset provides a structured workflow for Lattice Light-Sheet Microscopy image processing, including raw data acquisition (.czi), summarised data (extract the .zarr compressed file), metadata extraction, and image enhancement techniques such as deskewing and deconvolution that can be found as a script (main.py). The dataset is intended for researchers working with high-resolution microscopy data.

Contents

1. Raw Data: Original microscopy images in CZI format 

   • It is recommended to store the raw data (e.g., CZI files) as a baseline for reproducibility. If raw data is too large (e.g., 500 GB), consider downsampling it for testing and archival purposes.

2. Metadata: Embedded data extracted from Zeiss software can be found directly after processing .czi file, while external metadata is synthetically generated (https://github.com/onionsp/Synthetic-WGS-Dataset-Generator/).

3. Processing Scripts: Python scripts (as found in main.py) for deskewing, deconvolution, and data summarization.

   • Use the provided processing scripts to perform deskewing, deconvolution, and other preprocessing steps. Note that processed data can become significantly larger (e.g., a 500 GB raw dataset may expand to 700 GB after processing).

4. Summarized Data: Processed image outputs in .zarr/.tiff format, reducing storage overhead while maintaining key insights.

   • Save summarized data to reduce storage requirements. Summarized data could include key metrics, visualizations, or compressed outputs.

5. Data Transfer Agreement: Documentation regarding data sharing policies and agreements.

Workflow Overview

• Deskewing: Corrects image distortions caused during acquisition.

• Deconvolution: Enhances image clarity and sharpness.

• Downsampling: Reduces resolution for efficient processing and sharing.

• Conversion: CZI to Zarr or TIFF format for optimized storage and computational use.

Data Access & Usage

• The dataset, including raw and processed files, is hosted on Zenodo.

• Users are encouraged to download downsampled versions for testing before using full-resolution data.

• Processing scripts enable reproducibility and customization for different research applications.

• Data transfer policies are outlined in the included Data Transfer Agreement.

https://github.com/DBK333/Omero-DataPortal/tree/main/OmeroImageSamples

https://github.com/BioimageAnalysisCoreWEHI/napari_lattice