From Specimens to Datasets: Robust, Reproducible, and Re-use Ready
Workshop Schedule
- Introduction to CT & NoCTURN
- Specimen Preparation & Data Acquisition
- Image Stack Manipulations
- Data Management & Storage
Followed by a Panel Discussion with Q & A
Pre-Workshop Activities
Hardware Check: If you want to participate in software demos, please bring your own laptop or notebook computer. Your device should run Windows, Linux, or Mac OS (a modern file system is needed for the planned activities). There are no minimum hardware requirements for your device.
Download Software: Download & install Fiji (ImageJ) and 3D Slicer
Download Datasets: Download one ZIP file with two datasets (500 MB). We will use these two sample datasets during the workshop: one is a diceCT fetal badger, and the other is a racoon skull. Each dataset is small (< 300 MB) to ensure accessibility of the workshop to any configuration of Windows, Linux, or Mac OS computer.
Resources Discussed During the Workshop
Workshop Slide Deck (1.45 GB ZIP file)
NoCTURN CT Reference Vocabulary
MICRO example Scan Request Form
MICRO recommendations for sample packaging
MICRO guidelines for using Fiji (ImageJ) to Manipulate Image Stacks
White House Office of Science and Technology Policy 2022 Nelson Memorandum
NoCTURN World Map of CT Facilities
NoCTURN Exemplar Data Management and Sharing Plan
NoCTURN Recommended Repositories for Data Sharing and Reuse
How to Use MorphoSource:
Insightful Manuscripts
Wilkinson et al., 2016 — The FAIR Guiding Principles for scientific data management and stewardship
Boyer et al., 2017 — MORPHOSOURCE: ARCHIVING AND SHARING 3-D DIGITAL SPECIMEN DATA
Jacobsen et al., 2020 — FAIR Principles: Interpretations and Implementation Considerations
NoCTURN Booth
Don’t forget to visit booth no. 10—the NoCTURN Booth—during the poster sessions for more swag and answers to all of your CT questions!