Resources & Data Transfer

Data Storage Policy

User data is the users' responsibility. User files left locally on UIC systems are not backed up and will be deleted as needed. 

The UIC provides data transfer server space so that users of the facility have a method to migrate files from our equipment to your lab’s data storage as per your data management plan. The purpose of the space 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 three months will be automatically deleted. If you need assistance please contact UIC staff.

Resources

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Resources

Data Transfer Servers

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, smb://nas.uic.umn.edu/user, and click connect. Connect as a Registered User with the Username: user  Password: transfer.

Windows (PC): From Windows Explorer right click on “Thic PC” and select  "Map network drive...". 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  Password: transfer

Place all data (folders or files) within the folder named "User Data Goes Here".

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.

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.

Learn more about UMN Google Drive.

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 drive..." 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.

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://uicem.ahc.umn.edu/em , and click connect. Connect as a Registered User with:
  • Username: emuser
  • Password: emtransfer
Windows (PC)
From Windows Explorer select "Tools" from the menu bar then select "Map network drive..." in the drop down menu. Enter the server address, \\uicem.ahc.umn.edu\em , and click Finish. Connect to the server using :
  • Username: emuser
  • Password: emtransfer

 

iLab Guides

UIC iLab

Jackson Hall Animal Transport Routes

PDF Map - Jackson Hall Animal Transport Route

Software Downloads

Fiji (Fiji is just Imagej)

Click here to download
  • A powerful free downloadable open source image processing package based on ImageJ.

Nikon NIS-Elements Viewer

Click here to download
  • 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

Click here to download
  • Application for viewing, enhancing and processing Zeiss .czi files.
  • To install, register with Zeiss and download and install ZEN.

Imaris Viewer

Click here to download
  • A free 3D/4D microscopy image viewer for viewing raw images as well as those analysis within Imaris.

Leica Application Suite X (LAS X)

Click here to download
  • Application to open images acquired on the Leica SP5.

QuPath

Click here to download
  • QuPath is an open, powerful, flexible, extensible software platform for whole slide image analysis.

Olympus Fluoview Viewer

Click here to download
  • 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

Click here to download
  • Application for viewing and converting Huron TissueScope LE pyramidal tiff files.
  • Compatible with Window operating systems.

Nyquist Rate & PSF Calculator

Mobile Apps

App Name: Resolution
Author: Andrew L. Barlow
Platforms: Android & Apple products
Cost: Free
Description: Characterize your microscope objective lenses, see how well matched they are to your microscope's image acquisition system. Input the magnification, immersion medium (air, oil, glycerol or silicone oil), NA (numerical aperture) and wavelength of light (lambda), to calculate the lateral resolution, axial resolution and fluorescence brightness of the objective. Characterize your acquisition system (camera pixel size, camera binning and additional magnification) to check if you're sampling at Nyquist frequency. Each of your objectives can be saved and easily restored, and shared with other microscopists via e-mail, MMS, Linked-In or even Facebook (why not?). The equations used for the calculations can be displayed by selecting the "Show Equations" option from the App bar menu. The sources of equations are referenced in the "About" box.
 
 
App Name: Koehler Tutor
Author: Andrew L. Barlow
Platforms: Android & Apple products
Cost: Free
Description: Learn how to set Koehler illumination on any microscope. Teach yourself, or teach others. The app simulates your microscope's controls and the images generated at the eyepieces, acting as a virtual microscope. The locations of the controls on your microscope stand are shown, and the correct way to use them is explained. Their effect on the image at the eyepieces is demonstrated.
Remembering all of the steps required to set Koehler illumination can be tricky, and this app will serve as a useful reminder whenever you wish to check that the configuration of your instrument is correct.

Setting Koehler illumination generates an evenly illuminated field of view, reduces stray light, and allows you to set the balance between resolution and contrast.

Specimen Preparation Protocols

Microwave Protocols

Clearing

Societies

External Microscopy & Imaging Links

Image Analysis

University of Minnesota Core Resources