Windows-RUMC-RTCMicroscopy 1.0.0

Windows-RUMC-RTCMicroscopy 1.0.0

Warning
Important! This image may only be deployed in Radboudumc workspaces. It is not permitted to deploy the template in a workspace of a different tenant. Thanks for understanding.
The RTCMicroscopy template for virtual machines (VMs) in the DRE is aimed at researchers wishing to process and analyse microscopy images. As such, the template comes with several popular image processing applications preinstalled.

The following applications are preinstalled on the template:
  1. Fiji, including several non-standard plugins
  2. Cellpose, including GPU support
  3. QuPath

Using the template to create a VM

The template can only be selected during VM creation, a template cannot be applied to an existing machine. To use the RTC Microscopy you will first have to add a new virtual machine based on that template to your workspace.

In the first step of configuring your new VM, you will be offered a set of operating system (OS) templates to choose from. The RTC Microscopy template is currently the right-most template under the header RUMC Templates and may only be partially visible (see image). If you hover your mouse over the button, it will show you the full name of the template.



Your second choice will be the VM series, this determines the strength of the machine. While any series is viable, the template is intended to be used with a GPU supported system and an Nvidia GPU in particular. The current selection of hardware configurations of the DRE (the Standard_NCx machines) fits perfectly for the RTC Microscopy template.

Info
Note: other (stronger) Azure GPU machines can be available on request through myDRE support. Just make sure that you request an Nvidia-supported machine (the NC family or some of the ND and NV families).

Adding required internet access

In the DRE, internet access is blocked by default. Because the programs installed on this template require internet access, you need to set up external access ('allowlisting') before being able to use these programs. This step allows internet access to specific websites and services for the entire workspace, and thus affects all virtual machines in it.
Warning
This can only be done by the Accountable or a Privileged member of a workspace.


In the myDRE portal, go to the External Access tab of your workspace. Use the Add website(s) button and copy+paste the following list of domains, then click Submit.

imagej.net
fiji.sc
biop.epfl.ch
mosaic.mpi-cbg.de
www.cellpose.org
oice.uni-erlangen.de
cellpose.readthedocs.io
qupath.readthedocs.io

If you wish to refer to the Fiji website from the DRE, the following two websites are also recommended for legibility:

global.discourse-cdn.com
jsdelivr.net

Using Fiji

Fiji is a version of the image processing and analysis application ImageJ aimed at handling scientific images. It is one of the premier applications for published methods on specialised image handling for scientific purposes in the bio-medical field. Fiji can also easily be extended with new plugins.

In order to use Fiji, you can simply click on the Fiji shortcut button on the VM desktop. Please be aware that this shortcut contains some extra instructions for Fiji to function properly, so starting Fiji in another way may fail to provide complete functionality.

In addition to the standard toolbox that Fiji already offers, the version available via this template comes with the following extra plugins pre-installed:
  1. 3DScript
  2. MorphoLibJ
  3. MOSAIC
  4. PTBIOP
  5. QuickFigures
  6. StarDist
  7. TrackMate (including Cellpose and StarDist support)
Advanced (optional)
Fiji functionality can be extended by adding plugins through the Update command. If you wish to add a plugin this way, make sure to check the update site in the Add menu. If the update site isn’t available in the current domain whitelist of the workspace, you will need to add it before you select the plugin in the update dialog of Fiji or Fiji will start complaining that the site isn’t available.

Example 1 The Mosaic Toolsuite is available via update site mosaic.mpi-cbg.de. This site must occur in the domain whitelist in order to be able to add the Mosaic plugin to Fiji in your workspace.

Please note that for external access only the domain of the website or service should be added to the allowlist. For example, the 3DScript plugin included in this template has as update site romulus.oice.uni-erlangen.de. To allow this site, just leave off the leftmost part of the site address. So, in this case, the domain to be allowlisted is oice.uni-erlangen.de and 3DScript can be installed just fine.

Using Cellpose

Cellpose is an application for detecting and segmenting cells in microscopy images by using specialised deep-learning-based AI. By being trained to specifically detect cells, the segmentation produced by Cellpose tends to be much more realistic than classic rule-based and manual methods in Fiji. Cellpose can handle both fluorescent and histology-based images. It can also be trained to further specialise on specific image sets.

Cellpose can be used by the two Cellpose shortcuts on the desktop. Use the shortcut simply called Cellpose for separate (2D) images and Cellpose - Zstack in case you wish to process a 3D image stack.

If you wish to use Cellpose through Fiji, the PTBIOP plugin will allow that. The plugin has already been installed, but on first use you will have to indicate where Cellpose is installed on this VM. In the Fiji/Cellpose dialog, fill in the path C:\Cellpose in the first field conda environment path. (Note that this must be done once for every new user)

Using QuPath

Qupath is an alternative/supplement to ImageJ specifically created for handling large pathology slides. By cleverly changing the needed detail in images when zooming in and out, it can handle images far larger than ImageJ/Fiji can without loss of precision or speed. Furthermore, it is better equipped to deal with standard (i.e. RGB) histology images. For more information, see here.

QuPath can be started via the shortcut on the desktop.

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