The University Imaging Centers offers a number of resources to transfer and work on your data post acquisition.
This page also contains links to sample preparation protocols and external imaging tools.
The University Imaging Centers provide drive space on our Transfer Servers so that users of the facility have a method to transfer files from our equipment to other computers or off line storage devices. The purpose of this or any storage space in the UIC is not for long-term storage or safe-keeping of your data. Please remove your files from any local computer or our servers as soon as possible so that others can use the space. As per policy files left on the UIC equipment for over 90 days will be deleted as needed. If you need longer-term storage or assistance in transferring your files, please contact UIC staff to make arrangements. Thank you.
Remote Access through VPN
If you are not using the University network you will need to connect via VPN to access our internal UMN transfer servers.
A VPN connection is not required to access Google Drive storage.
UIC DATA TRANSFER SERVERS
UMN Google Drive
With Google Drive, you can create and share files and folders online and collaborate with others on group projects. Files in Google Drive can be accessed from any smartphone, tablet, or computer.
NAS UIC Transfer Server
An easy way to migrate files, NOT store them.
To connect to our UIC transfer server please follow the directions for your OS.
OSX (MAC): From Finder select "Go" in the menu bar then select "Connect to Server.." in the drop down menu. Enter the server address, nas.uic.umn.edu/user, and click connect. Connect as a Registered User with the Name: user and Password: transfer.
Windows (PC): From Windows Explorer select "Tools" from the menu bar then select "Map network device..." in the drop down menu. Enter the server address, \\nas.uic.umn.edu\user, check "Connect using different credentials" and click Finish. Connect to the server using the Username: user and the Password: transfer
Place all data (folders or files) within the folder named "User Data Goes Here".
UIC micro PET/CT Transfer Server
An easy way to move files, NOT store them.
The UIC µPET/CT Transfer Server is for µPET/CT data transfer ONLY. Any unrelated files will be removed without notification.
To connect to the µPET/CT NAS transfer server from any University networked computer.
OSX (MAC): From Finder select "Go" in the menu bar then select "Connect to Server.." in the drop down menu. Enter the server address, smb://petnas-1260f-ccrb.ahc.umn.edu, and click connect. Connect as a Registered User using your UMN login and password.
Windows (PC): From Windows Explorer select "Tools" from the menu bar then select "Map network device..." in the drop down menu. Enter the server address, \\petnas-1260F-ccrb.ahc.umn.edu\petdata, when prompted for a user name and password, you will want to use your UMN login and password.
- If you are on a Windows machine not connected to the AD system you will need to modify your username as follows:
- ad\your UMN internet ID (your password will be your umn login password).
Electron Microscopy Transfer Server
This server is intended for transferring data from our TEM or SEM instruments. If you have acquired data using a different instrument please use a different server option.
- Username: emuser
- Password: emtransfer
- Username: emuser
- Password: emtransfer
Depending on your analysis or visualization needs, several vendors provide free viewing or “light” software packages. If you need more complex analytical features, we encourage you to download Fiji (Fiji Is Just ImageJ), a powerful free downloadable open source image processing package based on ImageJ.
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.
Zeiss ZEN Lite for TIRF and Spinning Disk Confocal
- Application for viewing, enhancing and processing Zeiss .czi files.
- To install, register with Zeiss and download and install ZEN.
- 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 SP5.
- QuPath is an open, powerful, flexible, extensible software platform for whole slide image analysis.
Olympus Fluoview Viewer
- This software will read the data captured by a FV1000/FV500/FV300. Images saved with the FV file format (OIF, OIB, FV Multi-Tiff) can be read.
- This software is intended for image reading. Image capture, measurement, analysis, 3D function, etc. can not be performed using this software.
- For Windows operating systems.
HuronViewer for TissueScope LE
- Application for viewing and converting Huron TissueScope LE pyramidal tiff files.
- Compatible with Window operating systems.
Nyquist Rate & PSF Calculator
Specimen Preparation Protocols
- Adhering suspended samples onto coverslips
- Coating coverslips with poly-lysine for cell culture
- Embedding of cell monolayers
- Embedding of cells in suspension
- Embedding of tissue samples
- Embedding of yeast in spurr resin
- Immunolabelling of LR white-gold sections
- Immunolabelling of ultrathin cryosections
- Preparation of cryosamples
- Immunofluorescence Mountant
- Blocking buffer for Immuno LM and EM
- Correlative LM/EM probes (Tsien Youtube video)
CCRB - Red Bag Waste Disposal
Please review the guidelines below in order to ensure the safe and efficient removal of waste from labs.
Red Bag Waste guidelines for CCRB are as follows:
- RED BAG WASTE needs to be double bagged.
- RED BAG WASTE needs to be a maximum of 15 pounds, an easy weight for staff to grab with one hand and hold away from the body while depositing into a cart for removal.
- RED BAG WASTE inner and outer bags need to be tied AND taped shut.
- RED BAG WASTE should then be placed in the LER Linear Equipment Room (equip hallways) outside immediate lab space. Please note that red bag waste is removed on Mondays, Wednesdays, and Fridays only if there are biohazard containers available for FM custodial staff to fill.
- RED BAG WASTE will not be picked up or handled by custodial staff if the bag is punctured. Lab occupants will need to re-bag any waste from a bag that has been punctured. To avoid this, please dispose of pipettes and other materials that may cause puncture in a manner to avoid this.
- RED BAG WASTE should not include any glass items that should be disposed of in the proper Sharps container.
- RED BAG WASTE must be placed in secondary containment trays for pick up to collect any leaks. These containers are not supplied by RBMS, so labs will need to purchase their own.
- Many options for red bag purchasing may be found at UMarket such as: 14828335
- Many options for containment trays may be found at UMarket such as: cx18999, cx18998, cx18997
- Red Bag Waste is expensive to the University. Please be mindful to only bag Biohazard waste in red bags, not normal waste.
Additionally, NORMAL WASTE should be disposed of mindfully. FM will need to be able to contain any waste within the garbage bag in the waste bin. If items are too large to be placed in the bin, they should be disposed of in a different manner.
Thank you for your cooperation regarding these Red Bag Waste guidelines. Together we can ensure the safe and efficient removal of all waste.
Please contact firstname.lastname@example.org(link sends e-mail) for additional information or concerns.
Additional DEHS Protocols
- Neuroglancer: WebGL-based viewer for volumetric data
- CATMAID (Collaborative Annotation Toolkit for Massive Amounts of Image Data)
- Napari: A fast, interactive, multi-dimensional image viewer for Python
- BigDataViewer: re-slicing browser for terabyte-sized multi-view image sequences
- Paintera: A general visualization tool for 3D volumetric data
- Publication: Visualizing and Interacting with Large Imaging Data
- Publication: Antibody Conjugated Oligonucleotides as a Platform for Cyclic Immunofluorescent Staining
- Publication: VIPER: A Genetically-Encoded Tag for Fluorescence and Electron Microscopy
- Publication: Simple Chemical Stains for Feature-Rish Super-Resolution and Cleared-Tissue Microscopy
Supplies and Vendor Links
Live Cell Antifade
- LiveLight(link is external)
- Evrogen DMEMgfp2(link is external)
- Note option to add Rutin (also available from sigma-aldrich) on last page of the pdf.
- Marker Gene Technologies: Opti-Klear Live Cell Imaging Buffer 1x
- Marker Gene Technologies: Opti-Klear Live Cell Imaging Buffer 5x
External Microscopy & Imaging Links
- Invitrogen / Molecular Probes Spectra Viewer
- Invitrogen / Molecular Probes Fluorescence Tutorials
- Nikon Objective Specifications
- Nikon MicroscopyU
- What's in the picture? The temptation of image manipulation
- The JCB will let your data shine in RGB
- Interactive Focusing and Astigmatism Adventures on the Web
- Biological Buffers Reference, from Sigma-Aldrich
- Fluorescence Recovery After Photobleaching
- Biopolis Dresden Imaging Platform (BioDIP)
- Nyquist Rate and PSF Calculator
- Selected Works of George McNamara
- Nikon Learn & Explore
- The Cell: An Image Library
- Cell Painting Wiki