Skip to main content

Smart Microscopy

Arkitekt was designed for the increasingly complex real-time microscopy workflows of today. To illustrate Arkitekt readiness for Smart Microscopy, we deviced this simply no-code example of a Smart Microscopy workflow to perform the 3D live monitoring of cell clusters with a 40X objective, while scanning a large field of view with a 20X objective.

In this workflow, the Micro-Manager open-source software (Edelstein et al. 2014) is setup for a multidimensional acquisition. The user then interactively sets up a grid of positions on large sample area (2.61mm x 2.61mm, corresponding to 4*4 stage positions) containing living fluorescent cells.

During the workflow defined positions are then acquired at 20X magnification every 30 minutes for 24 hours. For every acquired 20X magnification image, nuclei are then automatically segmented on a remote computer using the Stardist (Weigert et al. 2020) algorithm, and cell clusters are computed with the help of DBSCAN (Ester et al. 1996). When one or more of such identified clusters are detected, the ROIs central coordinates and dimensions are translated back to stage coordinates and sent back to the microscope. 3D stacks of these positions (25 planes, 0.5µm step size) are then collected at higher magnification (40X) on a well-adjusted cameroa ROI fitting the cell clusters size. After all the positive events are detected, acquired in 3D high-resolution and displayed on the web-interface, the next image is acquired at 20X magnification

The Smart Microscopy Workflow

Prerequisites​

Please read

We strongly suggest to go through the Getting Started guide before attempting to run this workflow. It will guide you through the installation of the Arkitekt platform and the setup of your first workflow, as well as how to install plugins and apps.

This workflow is designed to run on a microscope computer running Windows 10 as well as on a remote analysis computer that will power the Arkitekt platform and the image analysis. To enable GPU acceleration for the Stardist segmentation, the analysis computer needs to have access to a CUDA 11 enabled GPU (tested on Nvidia GeforceRTX 2080Ti). The microscope computer will need to be connected to the same network as the remote computer.

Acquisition Computer​

Additionally to run this workflow you will need to have the following installed on your microscope computer:

As well as the following plugins installed on your Arkitekt computer:

arkitektio-apps/stdlib:master
arkitektio-apps/segmentor:master
arkitektio-apps/reaktor:master

Installing the Workflows​

This Smart Microscopy workflow is composed of two smaller workflows, the Acquire Clusters workflow and the Multi Dimensional workflow. In Which the Acquire Clusters workflow will be nested in the Multi Dimensional workflow.

Acquire Clusters Workflow​

The Acquire Clusters workflow is the workflow that will acquire a 20X Image, segment it, detect cluster and send the coordinates to the microscope to acquire all clusters with a 40X objective. To install this workflow connect this website to you Arkitekt instance and click on the Import buttom below:

React Flow
Not yet with Fluss

A few things to note about this workflow:

  1. This workflow utilizes a pretrained Stardist model to segment the nuclei in the image. This model comes preinstalled with the Segmentor plugin, by changing this node with a Predict Stardist node you can use your own Stardist model.

  2. The parameters to the Cell Cluster Detection are Global Variables of the Workflow

Deploying the Workflow​

During the Deployment of the smaller workflow it is imperative that you name the workflow Acquire Clusters as this and the parameters of the workflow will be used by the Multi Dimensional workflow, to adequately detect the workflow. If you choose to name the workflow differently you will need to change the respective Acquire Clusters node in the Multi Dimensional workflow. You do not need to reserve this workflow, as it will be reserved by the Multi Dimensional workflow.

note

This imperative naming need is a current bug and will be fixed in a future release of Arkitekt.

Multi Dimensional Workflow​

The Multi Dimensional workflow is the workflow that will run the above workflow in a multidimensional acquistions for all position every X minutes for X hours.

React Flow
Not yet with Fluss

Once connected this pane will also give you an overview over the apps that still need to be installed, nodes in green have been installed, nodes in yellow still lack an implementation. Of course feel free to explore this graph more interactively in your orkestrator interface

Test Environment

This workflow was tested on the following environments:


Acquisition Computer:

  • Intel Xeon CPU E5-2620 v4 @ 2.10GHz
  • 128GB RAM
  • Nikon Ti2-E Microscope
  • Windows 10
  • Micro-Manager 2.0.1 2023.05.23
  • MikroManager 0.0.1

Analysis Computer

  • Intel(R) Core(TM) i9-10900KF CPU @ 3.70GHz
  • Ubuntu 22.04
  • Arkitekt Paper Channel
  • Segmentor Plugin 0.3.4
  • Stdlib Plugin 0.3.9