Reporting & Reproducibility in Microscopy

Introduction to collecting and reporting microscopy metadata (5 topics )

User, Staff beginner

12 mins 10 secs

Last updated 2 weeks ago

This module invites you to learn the basics behind collecting and reporting microscopy metadata including guidelines and tools.

Introduction & module overview

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.

Introduction to community guidelines and tools for collecting and reporting microscopy metadata

Presenter: Caterina Strambio De Castillia, UMass Chan Medical School, Worcester, USA

Introduction to community guidelines and tools for collecting and reporting microscopy metadata - Topics

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

Towards community-driven metadata standards for light microscopy: tiered specifications extending the OME model

Open access Nature Methods article describing community-driven metadata standrds for light microsopy.

Source material

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

Micro-Meta App: a software for collecting microscopy metadata (20 topics )

User, Staff intermediate

49 mins 36 secs

Last updated 2 weeks ago

This module invites you to learn how to use Micro-Meta App, a free open-source software for collecting microscopy metadata.

What is Micro-Meta App?

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.

Micro-Meta App: an interactive tool for collecting microscopy metadata based on community specifications

Open access Nature Methods article describing Micro-Meta App.

Micro-Meta App tutorial

A step-by-step written tutorial explaining how to get started with the Micro-Meta App.

Micro-Meta App website

Download and learn more about Micro-Meta App at the link above.

Example microscopy metadata JSON files

Download example metadata files at the link above to test Micro-Meta App.

Introduction to collecting and reporting microscope metadata with Micro-Meta App

Presenter: Caterina Strambio De Castillia, UMass Chan Medical School, Worcester, USA

Introduction to collecting and reporting microscope metadata with Micro-Meta App - Topics

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

Outline of the Micro-Meta App workshop

Presenter: Caterina Strambio De Castillia, UMass Chan Medical School, Worcester, USA

Outline of the Micro-Meta App workshop - Topics

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

Installation of Micro-Meta App

Presenter: Caterina Strambio De Castillia, UMass Chan Medical School, Worcester, USA

Installation of Micro-Meta App - Topics

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

Managing an instrument in Micro-Meta App: Part 1

Presenter: Caterina Strambio De Castillia, UMass Chan Medical School, Worcester, USA

Managing an instrument in Micro-Meta App: Part 1 - Topics

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

Managing an instrument in Micro-Meta App: Part 2

Presenter: Caterina Strambio De Castillia, UMass Chan Medical School, Worcester, USA

Managing an instrument in Micro-Meta App: Part 2 - Topics

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

Managing settings in Micro-Meta App: Part 1

Presenter: Caterina Strambio De Castillia, UMass Chan Medical School, Worcester, USA

Managing settings in Micro-Meta App: Part 1 - Topics

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

Managing settings in Micro-Meta App: Part 2

Presenter: Caterina Strambio De Castillia, UMass Chan Medical School, Worcester, USA

Managing settings in Micro-Meta App: Part 2 - Topics

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

Source material

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

MethodsJ2: a script for Fiji to generate methods text (10 topics )

User, Staff intermediate

29 mins 23 secs

Last updated 2 weeks ago

This module invites you to learn how to use MethodsJ2, a Python script for Fiji for generating methods text for the use in publications and reports.

What is MethodsJ2?

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.

Introduction to methods reporting

Presenter: Joel Ryan, McGill University, Montreal, Canada

Introduction to methods reporting - Topics

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

Overview of MethodsJ2 Python script for Fiji

Presenter: Joel Ryan, McGill University, Montreal, Canada

Material required for the MethodsJ2 tutorial

Presenter: Joel Ryan, McGill University, Montreal, Canada

MethodsJ2 tutorial

Presenter: Joel Ryan, McGill University, Montreal, Canada

MethodsJ2 tutorial - Topics

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 GitHub repository

Download and learn more about MethodsJ2 Python script at the link above.

MethodsJ2: a software tool to capture metadata and generate comprehensive microscopy methods text

Open access Nature Methods article describing MethodsJ2.

Source material

MethodsJ2 tutorial: Advanced BioImaging Facility YouTube Channel

Recommended Metadata for Biological Images (REMBI) (23 topics )

Staff beginner

34 mins 6 secs

Last updated 2 weeks ago

Recommended Metadata for Biological Images (REMBI) is a draft of metadata guidelines within light and electron microscopy proposed by EMBL’s European Bioinformatics Institute (EMBL-EBI) and colleagues at over 30 other institutions in different bioimaging communities, including light, electron and X-ray microscopy communities.

REMBI aims to enable wider sharing and reuse of bioimaging data and is planned to be adopted by the BioImage Archive, EMPIAR, Cell-IDR and Tissue-IDR databases.

What is REMBI?