Storage and image analysis capacity at the LCI Core Facility
On this page you will find information on how to access, store, share your data at the Live Cell Imaging Core Facility.
How to store data
The Karolinska Institutet storage space (L, P or G drives) is automatically backed-up by the IT office. You will have access to your storage space as long as you work at KI. This is independent of the Live Cell Imaging Core Facility.
The KI storage space is fast and appears as an extra drive on your computer but without taking any space on your local hard drive. It is free of charge up to a certain amount, decided by the IT office. There is no size limit for the files. Files on the KI drives can only be shared with KI affiliated people.
Available drives at KI
To get access to any of the drives, contact the IT Support at KI. Inform them who else should have access to your drive. Once you get a confirmation email from the IT office, follow the mapping instructions to access your drive from any computer, including the VDI or LCI Remote desktop.
How to access your data from any computer
To access your KI storage space from any computer, you need to Map your KI drive to the computer. This only needs to be done once and can be done on any computer, inside or outside KI, including the VDI and LCI Remote Desktop.
VPN connection is required if the computer is not physically plugged (via ethernet cable) into the KI network. You then need to log in with your KI credentials to access your folder. Remember to type "user\" before your KI-ID.
How to connect to VPN
How to map your KI drive
For PC
- Open any folder
- Right click on This PC (on the left)
- Select Map network drive
- Under Folder, write the following: \\user.ki.se\labs (L drive) or \\user.ki.se\projects (P drive)
- Tick in Reconnect at Sign-in
- Click Finish
- Log in using your KI credentials. Remember to write "user\" before your KI id.
For Mac
- In Finder - go to Connect to Server
- In the connection window, connect to the following address: smb://user.ki.se/
- Log in using your KI credentials but r emember to write "user/" before your KI id
The LCI core facility has two types of remote servers for image analysis: The VDI and the LCI Remote Desktop. Both of them can be accessed from any computer. The VDI can be accessed from a mobile phone.
How to access the VDI to analyse your data
The VDI are part of the LCI service. You get access via the LCI staff.
The VDI is a Virtual Desktop Infrastructure with two machines called Remote Desktop Servers (LCI-1 and LCI-2). The VDI currently has free access for microscopy users.
Several users can access the RDS machines at the same time so the resources (RAM, GPU) are shared. If you think that an RDS is slow, click on Ctrl+Shift+Esc and go to the user tab. If someone uses a lot of (CPU) resources, work on the other RDS instead.
The servers are updated every third Monday of each month, between 05:30 and 06:00 so be sure that you do not have any analysis running at that time!
To enter the server, do the following:
- To access the VDI from outside KI premises, you need Two-step verification/MFA but VPN connection is not required.
- Download VMWare to your KI computer.
- Open VMWare, click on Add server and type "kivdi.ki.se"
- Log in with your KI credentials. Remember to write "user\" before your KI-ID.
To access your data on the VDI, map your KI drive.
You can save data on the desktop to run your analysis faster but delete them afterwards. We run regular automatic cleanings without warning.
The Fiji shortcut on the desktop will be replaced by us by a fresh install without warning. Do not use it if you need to download plugins. To use Fiji with more Plugins, install your own Fiji in your KI drive.
Please note that there are two ways to close the VDI: Sign out/log off or Disconnect:
- The normal way to stop working on the VDI is to Sign out/log off
- PC users: You need to select Disconnect and log off. Clicking on the cross on the bar will not sign you out
- Mac users: Click on the window sign at the bottom right of the screen. At the top right, right click on your name you get the Sign out option.
- The second way to close the VDI is to disconnect without logging off/singing out. This is only used if you want an analysis to keep running.
- Mac users: To disconnect, right click on the Power off button (Be careful not to click on Turn off or Restart!)
- If you connect from a mobile phone, you need to disconnect in the same way you would close a computer then you log out of the app by clicking on the electric plug sign.
How to access the Remote Desktop to analyse your data
The Remote desktop is a lot more powerful than the VDI and it is not shared (only one user at a time).
Note that Imaris has a free viewer available on the VDI that you can download to your own computer. Part of our service contract also includes free help from the Imaris specialists to create your own pipeline.
The VDI are part of the LCI service. You get access via the LCI staff.
You can download your data to the desktop to get a faster analysis but note that everything is automatically deleted from the Remote Desktop when you log off/sign out.
The LCI Remote Desktop is not free and must be booked in iLab. Check our fees.
To access the LCI Remote Desktop you will need an iLab account before doing the following:
- First time only: Make a request for access in iLab
- Book the Remote Desktop in iLab.
- Activate your booking in iLab by clicking on the Kiosk button
- A new page opens showing your booking: Click on the Start button
To access the Remote Desktop from outside KI premises, you need to be connected to the KI network via VPN.
Windows users:
- Open the Windows app called Remote Desktop connection
- Under Computer, type “h2vdigpu01.user.ki.se”
- Under Username, if you do not see your KI id, click Show options and enter "user\" and your KI-ID
- Click Connect
- If you get a security message about connection to remote desktop, click Allow.
- Enter your KI password + OK
Mac users: Download the Remote Desktop app. Make sure to give us more instructions and screenshot if anything is missing for Mac.
Please note that there are two ways to close the Remote Desktop. Note that all data are automatically deleted from the Remote Desktop when you log off/sign out.
- The normal way is to log off/sign out. Click the Windows button and click your account name. Select “Sign Out”.
- If you have an on-going analysis and you want to keep using the Remote Desktop without being connected with your computer, close the Remote Desktop window without closing the software. NB! You will be charged until you fully log off/sign out.
How to share your data with others
Data on KI drives
If you have an on-going analysis and you want to keep using the Remote Desktop without being connected with your computer, close the Remote Desktop window without closing the software. NB! You will be charged until you fully log off/sign out.
Data on KI drives can only be shared with KI people by following the instructions below. To share with non-KI people, you can upload your data to OneDrive.
- Right click on the folder to be shared and select Properties
- Under the Security tab, Groups or user name, click Edit then Add
- Under Enter the object name, write the name of the person you want to share with (they must have a KI email) and click Check names
- The email of the person is found. Click OK
- Set the level of permission. If you only want them to be able to download, untick Write, Full control and Modify. If you want them to be able to add or remove data from the folder, tick in Write and Modify. If they have Full control, they can change permissions for anyone and can even delete the folder.
- If the person has a KI Drive, your folder will automatically appear in their KI drive. If not, contact IT helpdesk.
MTF
MTF is a server to share files with non-KI people. The data disappears automatically after a couple of days. The recommended way to transfer files is to upload them to the KI MFT server using a freeware called Filezilla.
It is possible to upload data to the MFT server directly but then the folder structure is not retained, so it is best to upload data via SFTP (with Filezilla).