Kjernefasilitet for avansert mikroskopi (KAM)


FAQ

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Subject

Question Answer

Access

How do I get access to the Advanced Microscopy Core Facility (AMCF).

The doors into AMCF are locked.
Your key card needs to be registered to open the doors.
Please send an e-mail to Tom-Ivar (tom-ivar.eilertsen@uit.no) that includes;

  • the endorcement of your principal investigator
  • your name
  • your department
  • your key card number (on the back of your key card)
  • the instruments you need access to
  • your PPMS registration (see below)

Access

Where can I update my ID card?

There are update boxes on the wall at level 8 by the west entrance at MH2 (near the GRUT coffee bar) and on level 7 (lysgården) in MH1.

Access

How do I get access to an instrument?

You need to book an instrument before you are allowed to use it, see below.

Booking

How can I book an instrument?

At AMCF we use a booking system called PPMS (Pasteur Platform Management System), and you will need to register as a PPMS user in order to use it.
PPMS will allow you to book instruments at AMCF from wherever you may be situated as long has you have an internet connection.
The PPMS user interface is a web page, thus it works on all units with a web browser installed, including smartphones and tablets.

Booking

How do I register as a PPMS user?

In your web browser, go to this web page and click on the AMCF link.
Click on the Account creation request link near the top of the page.
Start the registration process by choosing between:
           Your institution is UiT     or      Your institution is NOT UiT.
UiT users will be redirected to Feide login and then to the account creation request form.
You will need to choose between-, or provide the following information (all in English), so please look it up before you start the registration process (note that some fields are optional);

  • The name of your research group
  • The name of your department
  • The name and e-mail address of your principal investigator
  • Your personal/project financial account number (if you have one)
  • The default financial account number of your group
  • Your affiliation:
    • Helsefak users, choose: HF
    • UNN/clinical pathology, choose: Klin Pat
    • Department of Geology, choose: Geo
    • Others, choose: None

If you are the principal investigator of the group, check the box: I request management rights….

Click submit. Your account creation request will then be validated by AMCF staff, and you will be informed by e-mail when everything is ready.
When ready you can book instruments through the link given above.

NB: We strongly encourage principal investigators to register and claim management rights of their group.
This will allow tracking of expenditure, give access to draft invoices, usage statistics, and other useful features.

Booking

Why am I not allowed to book the instrument i want, even though I am a registered user on the PPMS?

Registering as a PPMS user doesn't automatically give you access to all instruments.
In PPMS you can only book instruments on which you have user rights.
User rights are granted per instrument based on whether you have been trained on that instrument, and will give you status as an autonomous user, i.e. o
nly autonomous users are allowed to book their instrument in PPMS.
If you are registered as a PPMS user, but not registered as an autonomous user of a particular instrument, you are only allowed to see the schedule for that instrument (click "Schedules" in the upper red bar on the PPMS web page).
In order to t
o book time on the instrument as a non-autonomous user, you must send an e-mail to the super-user of that instrument, asking for assistance and to be booked in.

As of october 2020 we don’t have a complete record of who has been trained on each instrument in the past before we started to use PPMS, thus your PPMS profile may initially be missing user rights on some instruments. If this is the case, send an e-mail to Tom-Ivar (tom-ivar.eilertsen@uit.no) and/or Kenneth (kenneth.larsen@uit.no) and tell us what you are missing.

Booking

Why am I not allowed to cancel my booking in PPMS ? 

The booking schedule inside PPMS is divided into time units, e.g. a half hour each.
Thus, if you want to book an instruments from say 09.00 to 11.00, i.e. 2 hours, you will need to book 4 x half hours.
You cannot cancel the half hour that you have already started on, e.g. if the time is 09.01 when you try to cancel your booking, it is impossible to cancel it, but you will be able to cancel the rest of the booked time from 09.30 to 11.00, i.e. the next three half hours.
If the time is 08.59 when you try to cancel your booking, it is possible to cancel all the booked time.

My data Why is the instrument PC not connected to the (AD-) network or internet, making it impossible for me to copy/tramsfer my data?

Operative system (MS Windows) updates are frequently sent out to all PC's connected to the network and these may sometimes induce compatibility issues and bugs regarding the installed software of the PC, e.g. the software that controls the instrument.
In the worst case scenario the software stops working.
An instrument PC is solely dedicated to controlling the instrument and doesn't need operative system updates.
However, it is possible for you to copy/transfer your data by other means; see below.

My data Why am I not allowed to connect a USB memory stick/portable drive to the instrument PC  in order to copy my data?

If your USB memory contains some computer virus, it could infect the instrument PC, in the worst case brick it, making it impossible for other people to use the instrument (the majority of people with computer viruses on their USB memory doesn't know).
However, it is possible for you to copy/transfer your data by other means; see below.

My data So, if the instrument PC is not connected to the network and I'm not allowed to use a USB memory, how can I get access to my data then? There is a folder on the instrument PC which is frequently made backup of (typically every 30 minutes).

If you want your data to be backed up, your data need to be in that backup folder.
The data in the backup folder will be stored on the ResearchData server storage, and they can easily be accessed there from your office PC; see these instructions for more detailed information.
Short version; in order to retrieve your data, e.g. from the ResearchData server storage to your personal PC / office PC, use a FTP client like FileZilla which will list all the instruments at the core facility.

In FileZilla you can navigate to the relevant instrument and find your personal folder with your data, then download your files to your personal computer.
If you are on a PC outside of the UiT network you need to log on via VPN first in order to access the FTP server.

Warning: Data stored elsewhere (e.g. on the instrument PC desktop) may be deleted without notice!

My data How can I get Filezilla? See these instructions on how to do download FileZilla, and how to use it.
Software: FlowJo How do I run FlowJo on my own PC? FlowJo is licensed software for analyzing and visualizing (publication quality) flow cytometry data.
Download FloJo to your PC from this website and authenticate it by signing in with a license number.
AMCF has five license numbers, and you can rent one of them for one month at the time by sending an e-mail to Tom-Ivar (tom-ivar.eilertsen@uit.no).
AMCF also has a stationary PC in room L.09.323 with FloJo installed (authenticated by a dongle) which is offered to users that don't want to install FlowJo.
Software: Volocity How do I run Volocity from my own PC?

Download legacy versions of Volocity from Quorum Technologies. Note that ver. 6.3.1 is the last available version of the program (released in 2013) and it may not work properly on new PCs.

Next, contact the staff at AMCF to create a personal user on our Volocity server.

Install and run Volocity on your PC (you may need administrative privileges). On startup, choose the server option and fill in lisens-volocity.uit.no and port 15002.

When prompted, fill in your Volocity user name and password, and choose one of the available configurations from the dropdown list. The program should now start.

NB! Remember to exit the program when you are done so that the license becomes available for someone else.

Instruments: Flow cytometers  What are the differences between the flow cytometers?  See this page.
Instruments: Slide scanning Where can I find my virtual slides after scanning? You can find them in OlyVIA web at olyvia.uit.no. Log on with your UiT user name and password, choose database "test", check "Windows Authentication" and type "ad.uit.no" in the domain field. Note: For the time being you need to be on a UiT network or connected via VPN for OlyVIA web to work.