In addition to being an active research lab on the UW-Madison campus, the Laboratory for Optical and Computational Imaging (LOCI) initiates quite a lot of experimental instrumentation techniques and develops software to support those techniques. One major database platform development is OMERO, which stands for Open Microscopy Environment Remote Object. OMERO is an open, consortium-driven software package that is set up with the capabilities to view, organize, share, and analyze image data. One hiccough is that it’s not widely used at LOCI.
Having identified this problem, my mentor Kevin Elicieri, LOCI director, and I thought it would be a good idea for me to develop expertise in this software as a project for ZOO 699 and figure out how to incorporate it into a researcher workflow at LOCI. On-site researcher Jayne Squirrel was the ideal candidate as she is a highly organized researcher working in the lab, providing us an excellent use case. Before we could insert OMERO into her workflow, we had to lay some formal foundational management practices, which will be transferable in her use of OMERO.
We identified four immediate needs:
- Simple and consistent folder structure
- Identify all associated files
- ID system that can be used in OMERO database
We then developed solutions to meet each need. The first solution was a formalized folder structure, which we chose to organize by Jayne’s workload:
This folder structure will help organize and regularize naming of files and data sets not only locally and on the backup server, but also within the OMERO platform.
In order to identify all files associated with a particular experiment we developed a unique identifier that we termed the Experiment ID. This identifier will lead file names and consists of the following values: initial of collaborating lab (O or H) and a numerical sequence based on current year, month, series number of experiments, and replicate.
The example reads Ogle lab, 2014, November, second experiment (within the month of November), replicate one. Incorporating this ID into file names will help to identify and recall data sets of a particular experiment and any related files such as processed images and analyses.
Further, both the file organization and experiment ID can aid organization and identification within OMERO. The database platform has two levels of nesting resolution. The folder is the top tier; within each folder a dataset can be nested; each dataset contains a number of image data. So, we can adapt folder structure naming to organize files and datasets and apply the unique identifier to name uploaded image objects. These upgrades make searching more robust and similar in process to local drive searches.
Lastly, we developed documentation for reference. We realized that Experiment ID’s need to be accessible at the prep bench and microscope. We subsequently created a mobile accessible spreadsheet containing information on each experiment. We termed this document the Experimental Worksheet and it contains the following information:
- Experiment ID
- Experiment Description
- Experiment Start Date
- Project Name
- Sub-project Name
This document will act as a quick reference of bare bones experiment information for Jayne and student workers. Too, we realized that Jayne’s student workers need to know what the processes are in each step of her workflow. So, we developed step-by-step procedures and policy for each phase of the workflow. These procedural and policy documents set management expectations and conduct for Jayne’s data. Now, with such a data management foundation laid, the next step is to get to our root problem, discern how Jayne can best benefit from using OMERO and where it makes sense in her workflow.