Demo

Three different demo workflows are provided in the demo

Please download the demo and read the following instructions. You can download the demo package here.

Open the VirtualBox file and double click the LifeXplorer icon on the desktop. 

You can choose now to test one of three demo workflows. After running on of them you need to close and reopen the software to run another workflow.


Workflows 

1. ARCO offline workflow

The following screenshot illustrates the final result of the ARCO offline worklow. To reach that result you have to perform the following actions:

1. Press "Send to network" to send the preconfigured ARCO offline workflow to the LifeXplorer processing network. 
    The LifeXplorer processing network w
ill be simulated locally and reconfigured to drive the specified workflow.

2. Press "Activate" - a message box will appear: "Processing start now".

3. Press "OK" for after several info boxes about the execution status will appear.
 

After that you just have to be a little patient. ARCO will optimize the data quality by reducing the phototoxicity costs and optimize the output, 

by finding a suitable data analysis with optimized parameters. You can follwo the progress of ARCO by reading the message boxes that will

appear in the demo and by checking the status in the status bar at the botton left:

StatusBar

 

One algorithm after another will be varified by ARCO and the user interface will finally look silimar to the following:

ARCO workflow

The processing will take a while and will be finished if a message box appears "Processing finished. Best result identified". 

You can follow the processing steps by looking at the output folder: C:\LifeXplorer\MicroscopeInterface.

As it can be seen in the screenshot below, each algorithm will be run with different exposure times and different parameter configurations.

Exemplarily only two different exposures times will be analysed: 1000 and 100 ms. 


FolderOutput

 

The result of each algorithm that maximizes the object count with the minimal exposure time possible, can be seen in the folder:

C:\LifeXplorer\MicroscopeInterface\_ARCO_Results. There three final result images appear. The red area in each image is the area 

that cannot be detected with the lower exposure time of 100ms. 
  

FolderOutput FinalResults


How is that done?

ARCO first optimzes the analysis parameters of each algorithm for the highest exposure time, here 1000 ms, in order to maximize the object count, here Golgi complexes. It then runs the algorithm again with all possible configurations within a given parameter range on the image with the lower exposure time, there 100 ms. The algorithm's parameter configuration will be taken which maximizes the area that overlaps with the reference result of the highest exposure time. After that all best results of the algorithms (here Global Thresholding, CellProfiler + ilastik and the MOSAIC particle detector) will be compared based on there object count to exposure time ratio. The result will be chosen that maximizes the object count / exposur etime ratio.

 

2. ARCO for Nikon microscopes

The overall system optimization workflow for Nikon microscopes look like the following:


ARCO workflow for Nikon microscopes


Similar to the other workflows, you will be lead through the workflow by message boxes and processing status information in the bottom.


3. Refocusing Trigger

The refocusing trigger sample workflow uses time series data. How the trigger logic works is explained on the application page.
Over time the focus can drift and once this happens a trigger is send to the microscope to refocus a certain position.
The workflow is very simple and looks like the following: 

RFT workflow

Once the image quality drops below 95%, relative to the image quality measured after the last focusing, the trigger is activated and the

microscopes perfoms a full refocusing step. Above 95% of quality always the focus is slightly changed by taken the image stack plane

with the highest quality. The data used for this demo workflow can be found under: C:\LifeXplorer\SampleData\Golgi_sample.


RFT triggered