Product overview
The DC18A – Microbial Imaging Facility Project supports accessibility, scheduling, management, monitoring and reporting of microscope sessions on the following instruments:
- Nikon Ti inverted epifluorescent microscope
- Nikon A1 laser scanning confocal microscope
The software provides a way for automatic capture of metadata at each microscope session, storage of research data and metadata in the university’s research data storage, export of research data to third party analysis software, enable research data files to be easily shared with colleagues and collaborators.
- Management of information about experiments and microscopes, and linking them to uploaded datasets.
- User management and provisioning plus permissions to control access to data.
The web application component allows the following functionality:
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User sign up for an account in the system
Researchers use their UTS Staff/Student ID to register an system account. Full name, email, department or institute, and supervisors info will be captured and stored. Once approved by administrator, they can use their Staff/Student ID and password to login and use microscopes.
Note: password is provided by UTS, this system will not request and store any password info. UTS authentication system will be used to let user login, i.e. researcher can login with the same id/password as login to windows workstations.
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Admin approve and reject account requests
Once new user registered, administrator will receive a registration request email. They can choose to approve or reject request. New user can login system once administrator approve.
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Admin activate and deactivate user accounts
Administrator can deactivate user. Deactivated user can not login to system until administrator reactivate the account.
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Create projects
Researchers can create project. Project metadata will be collected. Which includes: project Name, description, funding info, and supervisors on this project.
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Create experiments and save the experiment metadata
Researchers can create experiment only in the lab. Experiment metadata will be collected. Researcher can select project from existing project list, or create a new project. The microscope instrument information will be automatically displayed on the create experiment page. Researchers manually input other metadata to create experiment, which includes: experiment name, lab book number and page number, cell type or tissue, experiment type, apparatus, fluorescent proteins, specific dyes, immunofluorescence values.
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Download the metadata for an experiment as a CSV
Once successfully create an experiment, researchers can download a zip file. Which includes a datasets folder and a metadata file in CSV format.
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Download a summary report of the lab usage as a CSV
Administrator can download a summary report in CSV format which includes all experiments of all projects.
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Updating of user details
Users can update their details like email, supervisors.
Logon Script:
This script gets installed onto the instruments within the lab. This script will automatically display the logged in user the DC18A web app in kiosk mode when they login windows. If they are an active DC18A user they will automatically see the "Create Experiment" page. If not, they will see "Sign Up" page with their id pre filled in Staff/Student ID field.
Logoff Script:
This script gets installed onto the instruments within the lab. Once the logged in user "Logs off" or "Shutdown" from windows they will automatically be displayed a feedback form. Once the feedback is submitted the "Log out" or "Shutdown" process will continue normally. The experiment session time will be recorded in metadata.
a lack of basic metadata collection at microscopy image acquisition time
researchers and facility administrators
data loss; complicated reporting; and duplicated data collection
- to capture crucial metadata concerning the project, experiment, session and active user at microscope login time, prior to image acquisition;
- to provide reporting about microscope utilisation to facility administrators;
- to provide basic metadata to ANDS Research Data Australia to facilitate reuse by enabling the discovery of existing data collections.
This system is highly tailored to the Microbial Imaging Facility at the UTS. To try and reuse it in another context, work would be needed to remove (or modify) several of the existing features. The authentication system currently is using the UTS LDAP to authenticate users. The project and experiment metadata fields will also need to be modified as they are tailored to the specific instruments at the Microbial Imaging Facility.