Image analysis

Mac users

Download the Remote Desktop app. Make sure to give us more instructions and screenshot if anything is missing for Mac.

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

Please contact us to request help.

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/Mac 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

How to get started using Imaris

The Live Cell Imaging Core Facility (LCI) has a free viewer available on the VDI which can be downloaded to your computer. This free software enables you to open both native microscopy files and datasets already analyzed in Imaris. There is also a full version available on the Remote Desktop.

How to get started

Start by making a request in iLab, to get access to the LCI Remote Desktop and Imaris.

• Book Imaris in iLab and activate your booking
• Connect to the LCI Remote Desktop using the instructions in the guide found in the Image analysis software webpage on our website.
• Please be aware of the turn off procedure (see the desktop background image) for the LCI Remote Desktop, otherwise you will be charged more then what you use.
• Open the Imaris converter software and convert your data to the .ims format
• Open the Imaris software and upload your data in the .ims format. It appears in the Arena.

There are quite a few video tutorials about how to use Imaris. We recommend the video on Importing Data into Imaris, Object Detection in Imaris using Srfaces - Basic, Object detection in Imaris using Spots - Basic and 
Automatic Imaris 10 Filament Tracer Tree Autopath Walkthrough (Oxford Instruments).

Once you are a bit more familiar with Imaris and what it can do, you can ask for free support from the Imaris team to learn how to improve your pipeline or do things you do not yet know how to do.

To do so, send an email to eusupport_imaris@andor.com with your contact information, informing them that you currently work with the Imaris software at the LCI facility at Karolinska Institutet and explaining what you would like to to.