Reporting & Reproducibility in Microscopy

Rigorous record-keeping and quality control are required to ensure the quality, reproducibility and value of imaging data. The 4DN Initiative and BINA here propose Light Microscopy Metadata Specifications that extend the OME Data Model, scale with experimental intent and complexity, and make it possible for scientists to create comprehensive records of imaging experiments.

• Why are QC and documentation important for imaging experiments?
• What is needed to achieve appropriate QC and Documentation?
  • The importance of Research Data Management
  • What is image metadata?
  • What constitutes microscopy metadata?
• How can QC and documentation be done in the real world?
  • The 4DN-BINA-OME-QUAREP (NBO) Microscopy Metadata Specifications
  • Interoperable software tools are essential for QC, reporting, and reproducibility
  • How can you use image metadata in practice?
• Communities such as QUAREP-LiMi are essential to build consensus specifications and procedures

Introduction to Community Guidelines and Tools for Collection and Reporting Microscopy Metadata: Worcester Image Data Management YouTube Channel

Micro-Meta App is an intuitive, highly interoperable, open-source software tool that is designed to facilitate the extraction and collection of relevant microscopy metadata as specified by the recent 4DN-BINA-OME tiered-system of Microscopy Metadata specifications. In addition to substantially lowering the burden of quality assurance, the visual nature of Micro-Meta App makes it particularly suited for training purposes.

• Introduction
• Outline of the tutorial
• What information should be captured
• 4DN-BINA-OME microscope metadata specifications
• What is metadata model?
• How to document imaging experiments
• Introduction to Micro-Meta App

• Objectives of the tutorial
• Where to find instrutions on how to best take advantage of this tutorial

• Tutorial outline and instructions can be found on Protocols.io
• Where to find latest version of Micro-Meta App
• How to download and install Micro-Meta App

• Introduction
• Selecting the Micro-Meta App home folder
• Deciding which Micro-Meta App section to work on
• Launching "Manage Instrument"
• Choosing which documentation tier to use
• Importing an example microscope JSON file into Micro-Meta App
• Viewing and exploring metadata in Micro-Meta App
• Exploring general information about the microscope hardware specifications
• Exploring hardware specifications of the objectives
• Exploring hardware specifications of the filters
• Saving the imported JSON file to the home folder

• Introduction
• Launching "Manage Instrument" and choosing a documentation tier
• Choosing microscope canvas (upright or inverted)
• Entering general information about the microscope hardware specifications
• Saving the microscope JSON file
• Adding hardware components to be documented and saving your work
• Entering information about hardware specifications of an individual objective
• Managing filter sets and individual filters
• Entering information about hardware specifications of an individual filter
• Entering information about a filter set and associating individual filter with it
• How to change tier level for an existing microscope JSON file and entering information gradually

• Introduction
• Launching "Manage Settings" and selecting the appropriate tier to document the imaging experiment
• Opening files required for managing image acquisition settings
• Opening a microscope JSON file used for image acquisition
• Opening an image data file whose acquisition has to be documented
• Opening image acquisition settings JSON file
• Visualizing "Manage Settings" canvas
• Exploring and managing general image acquisition settings
• Exploring the pixels dimensions of the image
• Exploring and managing imaging environment and objective settings
• Exploring and managing available channels
• Inspecting the light path associated with fluorescent channels
• Inspecting general information about fluorescent channels

• Introduction
• Adding an additional channel to the settings file
• Selecting the light source that was used
• Selecting the detector that was used
• Adding light source acquisition settings
• Adding camera acquisition settings
• Entering general channel settings
• Conclusions

Micro-Meta App Workshop: Worcester Image Data Management YouTube Channel

MethodsJ2 is a Python script for Fiji and it helps researchers to write materials and methods text for microscopy experiments by sourcing experiment information from metadata, as well as information from a microscope hardware configuration file generated in Micro-Meta App. A draft experiment methods section text is generated by MethodsJ2 which can then be revised by a user and used in written manuscripts and reports.

• Importance of methods reporting, existing tools and further reading
• Why it is important to have complete microscopy methods section?

• Required files for the tutorial
• Brief overview of MethodsJ2 workflow
• Importing MethodsJ2 Python script into Fiji
• Running MethodsJ2 Python script
• Opening an image file using MethodsJ2
• Manually adding information about sample preparation in MethodsJ2
• Manually checking image dimensions
• Selecting a Micro-Meta App JSON file
• Selecting the correct microscope system
• Selecting the correct objective
• Manually adding information for individual fluorescent channels and camera settings
• Selecting optional devices used during an experiment
• Adding ackowledgements

MethodsJ2 tutorial: Advanced BioImaging Facility YouTube Channel