Policies

Policies for Safe and Shared Use of AMCF Equipment

1. Hours of operation are typically 8am to 7pm with opportunities to book staff available time in advance, 5 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 (8p – 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.

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.
• New users and/or those who have not used the facility in 6-12 months must accumulate at least 20 hours of daytime use, display proficient and safe operation, and receive permission from AMCF staff to be approved for independent access on nights and weekends..
• 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

Instrument Policies: All Instruments

1.    No hazardous materials (biological or chemical) may be brought to the imaging core. If your samples are classified as anything other than Biological Safety Level 1 (BSL1), researchers must discuss samples with AMCF staff and/or Director prior to bringing them for imaging. Please see AMCF’s Biosafety summary.

2.    No Protected Health Information (PHI) may be collected or shared with or within the AMCF. Researchers are responsible for ensuring no PHI is contained in data collected and/or analyzed in the AMCF.

3.    AMCF users are obligated to fully acknowledge the facility and its funding sources in formal publications and presentations containing any data generated in the facility. See acknowledgement section below.

4.    Researchers are responsible for their data once it is collected (i.e. data should be immediately transferred to another location). Please use the OMERO server to safely transfer and store your imaging data. Everything that happens to your data after collection (i.e., analyses) is the researcher’s responsibility. Data temporarily stored on AMCF acquisition workstations must be organized in folders labeled as last name, first name.

5.    Researchers must remove oil, return the turret to the 10x objective, and lower the objective to the lowest position at the end of their imaging session to prevent damage to objectives between researchers.

6.    New users and/or those who have not used the facility in 6-12 months must accumulate at least 20 hours of daytime use, display proficient and safe operation, and receive permission from AMCF staff to be approved for independent access on nights and weekends.

7.    See data management and sharing plan for more information about data types, handling, transfer, and storage.

8.    Please review AMCF’s policies statement.

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. Starting January 2024, all AMCF facilitated data transfers will be to the AMCF OMERO server. Data temporarily transferred using SharePoint is subject to automatic removal after 1 year. Data temporarily stored/transferred using BOX may remain there, it is the responsibility of the researcher to establish long-term data storage for these files. The AMCF recommends researchers move images collected prior to 2024 to the AMCF OMERO server.

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 2024, the following data storage and handling capabilities are available.

Zeiss 710, 800, Elyra, CD7 acquisition workstations: Data may be temporarily (≤ 3 months) stored on the acquisition computer data storage drive (not desktop). Data drives will be backed-up to the OMERO server once a month. No data left on these systems is guaranteed to be safe from loss, researchers are encouraged to backup data at time of acquisition and/or upload their data to the OMERO server as soon as it is generated. The AMCF will allow data to remain (only in the appropriate ‘data drive’ location) on individual acquisition workstations for up to 3 months. After this time (or improperly stored data) will be removed from the acquisition workstations without prior notification. Data not 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.

Axioscan 7 Whole Slide Scanning, UltraMicroscope II Light Sheet Microscope acquisition workstations: These systems are currently connected to the internet.   Data may be temporarily (≤ 3 months) stored on the acquisition computer data storage drive (not desktop). Data drives will be backed-up to the OMERO server once a month. No data left on these systems is guaranteed to be safe from loss, researchers are encouraged to backup data at time of acquisition and/or upload their data to the OMERO server as soon as it is generated. The AMCF will allow data to remain (only in the appropriate ‘data drive’ location) on individual acquisition workstations for up to 3 months. After this time (or improperly stored data) will be removed from the acquisition workstations without prior notification. Data not 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.

Image Analysis Workstations (HALO, IMARIS):  These systems are currently connected to the network.  IMARIS rendered images (*.ims) are new images that may be stored on the OMERO server. Researchers may upload their own *.ims images to the OMERO server for back-up, storage, and sharing. HALO analyses do not modify initial images, instead a relational database (folders) store analysis parameters. HALO analyses are not compatible with the OMERO server architecture and should be stored elsewhere by the researcher.  No data left on these systems is guaranteed to be safe from loss, researchers are encouraged to backup data at time of acquisition. Data may reside on the acquisition workstation for 6 months. After this time (or data not stored on the designated ‘data’ drive) will be removed from the acquisition workstations without prior notification. This is not a guarantee of data safety nor security on these workstations.

Long-Term Data Transfer and Storage Plans (underway, NOT currently implemented): The AMCF worked with RITO to establish long-term biomedical image storage, management, and universal data sharing server using the OMERO platform, see below. OMERO is a critical organizational infrastructure for managing imaging data, is 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 raw imaging data collected on our imaging Shared Research Resource acquisition workstations, and can organize curated datasets with meta data meeting community standards for biomedical imagery. The OMERO server will read and organize meta data contained within biomedical images from hundreds of different systems (both inside and outside the imaging Shared Research Resource). More information about OMERO can be found at https://www.openmicroscopy.org/omero/