Image analysis

Note:

• To access your data on the Multi-user Remote desktop, 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.
• Imaris has a free viewer available as well as an Imaris File Converter on the Multi-User Remote desktop 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.

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.

1. The normal way is to log off/sign out. Click the Windows button and click your account name. Select “Sign Out”.  
2. 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. 

Single-user remote desktop

Single-user remote desktop is for one user at a time only and it is much more powerful than the Multi-user remote desktop. There is a fee for using this remote desktop.

• Imaris full licence, ImarisFileConverter, ImarisViewer
• M2 Deconvolution
• NIS Element full licence: AI, visualization, including of High content data (JOBS), STORM and image analysis
• ImageJ/Fiji: image processing and visualization freeware
• Omero: Data management freeware
• CTFire: analysis of polarization microscopy images freeware
• QPath:  open source software for digital pathology and whole slide image analysis
• Ilastik: open source analysis software
• Napari: is a Python library for n-dimensional image visualisation, annotation, and analysis. 

How to access the Single-User Remote Desktop to analyse your data

The Single-User Remote desktop is a lot more powerful than the Multi-User Remote desktop and it is not shared (only one user at a time).

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 Single-User Remote Desktop is not free and must be booked in iLab. Check our fees.

To access the LCI Single-User Remote Desktop you will need to do the following (first time only):

• Make a request for access in iLab
• Send a request to IDAC to get your login activated by following the instructions in the document below. Also in this document you can read how to book the Remote desktop in iLab and activate your session in KIOSK.

To access the Single-User 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 “lci-singleuser.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.

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.

1. The normal way is to log off/sign out. Click the Windows button and click your account name. Select “Sign Out”.  
2. 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.
3. NB! You will be charged until you fully log off/sign out.

The LCI Core Facility in-house analyst can also help you build your analysis pipeline.

Please contact us to request help.