Transfer, Access, View, and Analyze Your Data
Data Transfer
In partnership with the Minnesota Supercomputing Institute (MSI), the UIC provides UMN researchers multiple methods to transfer files from our equipment and services to long term storage.
The UIC can also transfer data to external clients through Google Drive, Box Secure Storage, Globus-compatible cloud storage, and physical storage devices.
The table below outlines the most common data transfer methods for UIC instruments and services.
| Service | Optical & Small Animal Instruments | Electron Microscopy Instruments | Tissue Clearing Services | Spatialomic Services | Slide Scanning Services |
|---|---|---|---|---|---|
| UIC NAS Transfer Server | √ | ||||
| UIC COMET Transfer Server | √ | ||||
| UIC EM Transfer Server | √ | ||||
| MSI SURFS & Home Directories | √ | √ | √ |
Accessing Your Data
The way users access their data depends on the method of transfer. Users trained on UIC equipment will learn how to transfer data during their training. Service users will receive an overview of the data pipeline at intake and additional instruction once their data is ready for viewing or delivery.
Remote Access:
To access UIC data transfer servers or MSI and OIT storage solutions off-campus, users will need to connect to the University's network via Virtual Private Network (VPN).
UIC NAS Transfer Server
Accessing the UIC NAS Transfer Server
The purpose of the server is for transfer, not storage, of your data. Please remove your files as soon as possible so that others can use the space. Files left on our transfer server for over 90 days will be automatically deleted.
UIC COMET Transfer Server
Accessing the UIC COMET Transfer Server
The COMET transfer server is intended for transferring and short-term storage of Lunaphore COMET data so it can be analyzed on UIC analysis workstations. It is not intended for long-term storage. Please remove your files as soon as possible to that others can use the space. Any unrelated files will be removed without notification.
UIC EM Transfer Server
Accessing the UIC EM Transfer Server
This server is intended for transferring data from our TEM or SEM instruments ONLY. Any unrelated files will be removed without notification.
MSI SURFS & Home Directories
Accessing MSI SURFS Data Delivery & Home Directories
MSI Shared User Research Facilities Storage (SURFS)
The UIC utilizes MSI's SURFS for delivering Tissue Clearing, Spatialomic, and Slide Scanning service data to UMN researchers.
MSI Home Directories
Through SURFS, the UIC delivers data to researchers group shared home directory space. Data will be stored for one year from the time of delivery in the SURFS data_delivery/uic directory. Researchers are responsible for migrating their data from the data_delivery/uic directory to their group shared space to ensure long term storage.
Access to MSI resources is available to Principal Investigators (PIs) and their research groups. For more information about access to MSI resources, please visit the Getting Started with MSI link below.
MSI Links, Resources, and Guides
- Getting Started with MSI
- Accessing files in your group shared home directory space
- Transferring data stored in your group shared home directory space between computers
- How do I use Globus to transfer data at MSI?
Research Data Storage (RDS)
Research Data Storage (RDS) is managed by UMN OIT and provides professionally managed secure, replicated, shareable storage space on the University of Minnesota’s network. It is intended for research data that is actively being used (e.g. viewing and analysis).
The UIC RDS storage space is currently only utilized for select tissue clearing service users for viewing and analyzing their data, and is typically only accessible through UIC analysis workstations at our facilities. Under certain circumstances, the UIC may authorize researchers to access the UIC RDS from non-UIC computers. To request access to the UIC RDS on non-UIC computer, please contact us at [email protected].
UIC User Guide: Accessing the UIC RDS storage space from a UIC Analysis Workstation
Viewing & Analyzing Your Data
Alongside our fee-based image analysis services, the UIC provides researchers with high-performance analysis workstations at each of our three locations. UIC analysis workstations feature advanced hardware, are connected to the UMN Gopher Science Network (GSN), and include a comprehensive suite of free and licensed image analysis software—enabling users to visualize and analyze their data.
UIC image analysis workstations are available for UIC users to use at no additional charge.
Reserving UIC Analysis Workstations
To reserve time on a UIC analysis workstation, users must have an active iLab account. Calendar access is granted by UIC staff upon request. Once access is approved, users can independently schedule time on a workstation. Please note that reserving a workstation does not guarantee staff availability. If assistance is needed, users must coordinate separately with UIC staff.
Current users with questions regarding workstation access should contact UIC staff at [email protected]. Researchers who are not current users but wish to utilize UIC analysis workstations should submit a request for access; a UIC staff member will follow up to discuss your analysis needs.
Reserving Imaris
Due to the high licensing costs and limited number of licenses available for Imaris, users interested in using this software must reserve both the software and the workstation they intend to use it on. This ensures availability and helps prevent scheduling conflicts when multiple users need access to Imaris at the same time.
The table below provides a summary of the various software packages available for users to use on UIC analysis workstations.
| Workstation Name | Minnetonka | Fenske | Sawbill | Superior | Itasca | Jitterbug | Manomin |
|---|---|---|---|---|---|---|---|
| UIC Facility | CCRB | CCRB | CCRB | CCRB | Jackson Hall | Jackson Hall | Snyder Hall |
| GSN Connected | √ | √ | √ | √ | √ | ||
| MS Office | √ | √ | √ | √ | √ | √ | √ |
| Nikon Elements* | √ | √ | √ | √ | √ | ||
| Nikon Elements Batch Denoise and Deconvolution | √ | √ | |||||
| Imaris | √ | √ | √ | √ | √ | ||
| FIJI | √ | √ | √ | √ | √ | ||
| HuronViewer | √ | ||||||
| AtoMx | √ | ||||||
| HORIZON | √ | ||||||
| Amira 3D | √ | ||||||
| AutoQuant | √ | √ | |||||
| QuPath | √ | ||||||
| MATLAB | √ | √ | √ | ||||
| VivoQuant | √ | √ | |||||
| CellProfiler | √ | √ | |||||
| Incucyte | √ | √ | |||||
| Living Image | √ | √ | √ | ||||
| Vevo LAB | √ | ||||||
| ilastik | √ | √ | √ |
*The modules available for Nikon Elements varies between workstations. For more information about specific modules, please contact [email protected].
View & Analyze Your Data Using MSI’s Advanced Computing Resources
Through MSI, UIC users have the option to access and interact with their data via Open OnDemand or a Citrix Windows Virtual Machine. These advanced platforms allow researchers to work with large datasets by leveraging the high-performance computing resources of MSI’s supercomputing clusters—all from their own laboratory or personal device.
User guides for opening UIC slide scanning data using MSI Open OnDemand
User guides for opening UIC tissue clearing data using MSI Citrix & Open OnDemand
Additional Software Resources
Software Downloads
Fiji (Fiji is just Imagej)
- A powerful free downloadable open source image processing package based on ImageJ.
Nikon NIS-Elements Viewer
- NIS Elements Viewer for PC and Mac is a free, "light" proprietary software for viewing images collected on several of our Nikon microscopes.
- Application for viewing and converting (.tif) Nikon .nd2 files.
Imaris Viewer
- A free 3D/4D microscopy image viewer for viewing raw images as well as those analysis within Imaris.
Leica Application Suite X (LAS X)
- Application to open images acquired on the Leica microscopes.
QuPath
- QuPath is an open, powerful, flexible, extensible software platform for whole slide image analysis.
HuronViewer for TissueScope LE
- Application for viewing and converting Huron TissueScope LE pyramidal tiff files.
- Compatible with Window operating systems.
Nyquist Rate & PSF Calculator
- Scientific Volume Imaging provides a free online Nyquist Rate and PSF Calculator.
- They also offer a downloadable android app.
Need help?
UIC Support Email:
[email protected]
MSI Support Email:
[email protected]