Policies

Policies for Safe and Shared Use of AMCF Equipment

1. Hours of operation are typically 8 am to 4:30 pm with opportunities to book staff available time in advance, 4 pm to 7 pm on Tuesdays and Thursdays.
2. Researchers may schedule an appointment by phone (402-559-6659) or email to facility staff.
3. Researchers that are fully trained and capable of displaying safe system operations are permitted to schedule independent reservations after hours (6p – 7a) and on weekends.
   • Contact core staff to request scheduling permissions in RSS and after-hours card access.
   • The core submits requests for card access. We highly recommend confirming card access is functional prior to arriving for afterhours imaging.
   • Researchers are expected to schedule times and instruments appropriately. Computer usage will be checked regularly, anyone using systems without permissions and/or reservations will lose access.
4. All UNMC researchers are welcome to independently schedule (RSS) and use the image analysis workstation in the data analysis workroom (DRC I Rm 1036).
   • Contact core staff to request RSS scheduling permission and card access to this area.
5. When COVID risk is high.
   • Saran wrap with a clean rubber band will be placed on each eyepiece by core personnel, to be removed and replaced after each user leaves.
   • After each use, microscope eyepieces and all touch surfaces will be disinfected with 70% ethanol.
   • All users entering the facility must don masks or face coverings over their mouth and nose.
   • Users should not come to the UAMCF or be on campus if ill.
     
     

Billing Policies

• All users must have a cost center number in the system prior to each period of use. This is required for automated billing.
• A minimum charge of 30 minutes will be billed for extended use and charged to the nearest 1/4 hour thereafter.
• Billing statements are issued monthly.
• Individuals must be trained, accrue 20 hours of assisted image acquisitions, and receive permission from core staff before unassisted (after regular business hours and weekends) will be permitted.
• If you cancel with less than 24-hours’ notice, you will be charged a fee of $30 to recover instrument set-up costs.
• If you arrive more than 15 minutes after your planned arrival, your first hour will be charged from the time scheduled, not the time of arrival. If you are more than 30 minutes late during high use periods, your time slot may be assigned to another user.
• If you overbook time (i.e., book three hours and use one hour), you will be charged for the full use period unless another user is available on short notice.
  
  

Instrument Policies

Super Resolution Imaging (ELYRA PS.1)

Structured Illumination Microscopy (SIM), Photoactivated Localization Microscopy (PALM), and Stochastic Optical Reconstruction Microscopy (STORM) are specialized techniques using delicate instrumentation requiring extended technical support from AMCF core staff. PALM and STORM require additional specialized sample preparations (see AMCF Imaging Resources).

1. SIM imaging can be conducted using traditional blue, green, short- and long-red fluorophores that are bright.
2. Users may bring SIM samples to core facility personnel for acquisition of images and basic processing. Core personnel will acquire images and process them (including dual/multi-channel alignments). Users will be able to view and choose the regions of interest that they wish to acquire.
3. With additional training, researchers can achieve independent imaging permission.
4. The core facility will provide basic processing and channel alignment and will allow users to choose how they would like data rendered and saved. Among these options are TIF images of a composite 3D SIM, individual TIFs of various z-sections, altered angles, planes, etc. as TIF images, 3D movies, etc. Please note: these image processing manipulations are complex and take time, yet they are an essential part of the SIM analysis thus are part of the core service (and charge).
5. First-time users may contact the core director for initial consultation/advise prior to using the facility. For each laboratory, this consultation will be free for the initial hour, but will be subject to the time and availability of the director.

Ultramicroscope II Lightsheet Fluorescence Microscope, Cell Discoverer 7

These systems are primarily operated by AMCF core staff. AMCF core users requiring extensive use are eligible for extended training to obtain independent operator status.  Researchers must complete extended training and display safe and proficient instrument operation before permission will be granted.

Axioscan 7, X-Clarity Tissue Clearing

These instruments are only operated by AMCF staff.

Data Management Policies and Procedures

Additional details may be found on the AMCF Data Management and Sharing Plan. 

Researchers are responsible for their data once it is collected (i.e. data should be immediately transferred to another location). Everything that happens to your data after collection (i.e., analyses) is the researcher’s responsibility.

Research data is stored in the file types described above (*.czi, *.ome tiff, *.ims).

Due to IT restrictions, temporary data storage on individual workstations is limited and variable across systems. As of January 2023, the following data storage and handling capabilities are available.

Zeiss 710, 800, Elyra, CD7 acquisition workstations: These systems are not currently eligible for automatic backup to a network location. All data should continue to be removed from the acquisition workstation at the time of generation. Data shall only be temporarily stored on the storage drive (not desktop) should researchers be unable to immediately transfer data. No data left on these systems is guaranteed to be safe from loss. The AMCF will allow data to remain (only in the appropriate ‘data drive’ location) on individual acquisition workstations for up to 4 months. After this time (or improperly stored data) will be removed from the acquisition workstations without prior notification. These data drives will be backed-up to an external drive once a month. Data not temporarily stored in the designated data drive location will not be backed up. This is not a guarantee of data safety nor security on these workstations. The AMCF is working with RITO to bring as many systems onto the network as possible. AMCF users will be notified via the email listserv regarding when each system is brought on-line. With active discussions underway regarding modified IT workflows for non-PHI data (i.e., all AMCF data) these updates will be prudently implemented as efficiently and quickly as possible while maintaining instrument operations. 

Axioscan 7 Whole Slide Scanning, UltraMicroscope II Light Sheet Microscope acquisition workstations: These systems are currently connected to the internet. Data may be securely transferred to individual researchers/research groups and/or temporarily stored (≤ 6 months) using the AMCF SharePoint location (contact James Talaska) or BOX account (contact Dr. Jensen-Smith). Data may reside on the acquisition workstation (3 months) and/or SharePoint/BOX location for up to 6 months. After this time (or data not stored on the designated ‘data’ drive) will be removed from the acquisition workstations without prior notification. Once a month, data will be backed up and/or fully transferred to a network location.  The AMCF is working with RITO to establish storage space for temporary transfer/storage of data (≤ 6 months) with the option for additional long-term storage for data from these workstations and/or between image acquisition and analysis workstations (estimated availability summer 2023).

Image Analysis Workstations (HALO, IMARIS):  These systems are currently connected to the network. Data may be securely transferred to individual researchers/research groups and/or temporarily stored (≤ 6 months) using the AMCF SharePoint location (contact James Talaska) or BOX account (contact Dr. Jensen-Smith). Data may reside on the workstation (up to 3 months) and/or SharePoint/BOX location for up to 6 months. After this time (or data not storge on the designated data drive) will be removed from the acquisition workstations without prior notification. Once a month, data will be backed up and/or fully transferred to a network location. The AMCF is working with RITO to establish storage space for temporary transfer/storage of data (≤ 6 months) with the option for additional long-term storage for data from these workstations and/or between image acquisition and analysis workstations (estimated availability summer 2023).

Long-Term Data Transfer and Storage Plans (underway, NOT currently implemented): The AMCF is working the RITO to establish additional temporary and long-term biomedical image storage, management, and sharing options using the OMERO platform. OMERO is a critical organizational infrastructure for managing imaging data, is universally/internationally accepted for publication-ready datasets, recognized by existing NIH data repositories, will allow us to eventually offer our own shareable data repository, directly reads/interfaces/integrates all imaging data collected on our imaging core acquisition workstations, and can organize curated datasets with meta data meeting community standards for biomedical imagery. The OMERO server will automatically read and organize meta data contained within biomedical images from hundreds of different systems (both inside and outside the imaging core). As soon as the OMERO server is active, researchers will be notified regarding specific features and storage options.

More information about OMERO can be found at https://www.openmicroscopy.org/omero/