Skip to main content


In this guideline, the integration process of a Leica STELLARIS 5 Confocal Microscope controlled via Leica Application Suite X ver.4.4.0 in Windows 10 into the Chemotion ELN is explained. The procedure is split into three aspects that can be set up independently or in parallel:

  1. Remote connection to the device
  2. Transfer of experiment data to the ELN.

General preparation aspects can be found here.

Considering all these aspects, this procedure has been conducted on the following system configurations. However it is likely to work on systems with different software versions as well.

Specifications of the device's PC​

  • Operating system: Windows 10
  • Software Name: Leica Application Suite X ver.4.4.0
  • Connected to LAN (Intranet only): Yes
  • Data files generated: *.jpeg
  • Static IP address has been configured


  • Remote Device Control
  • Data transfer to Chemotion ELN inbox


Remote Device Control​


General guideline regarding the configurations of remote device control can be found here.

Saving data for transfer​

After recoding the microscopy images, the scientist can analyze and evaluate them using the in Application Suite X software. To start the transfer of the finished files to the ELN inbox the finished project is saved to a transfer folder on the local computer (this transfer folder can be located anywhere the admin desires (Desktop, Documents, etc.). Data will then automatically be transferred from the transfer folder to the Chemotion ELN. The user is required to input a valid file output name according to the naming convention for the Chemotion ELN to sort the file into the correct user's inbox.


Please take care that you communicate name conventions to all users of the Chemotion ELN.

Necessary configurations in the microscope's computer​

Data transfer to the Chemotion ELN

The Leica microscope's computer and Chemotion ELN need access to a common network storage location. The network storage can be set up on a third-party storage (a NAS server, shared storage of another PC etc.). In this case, the LSDF storage service from KIT has been used.

An EFW executable needs to be configured, downloaded from the EFW builder and set to run on the device's PC. The EFW program will run on the device's computer in the background and transfer the finished projects from the transfer folder to the network location, accessible by both the device's computer and the ELN. Details can be found here.

Configurations in Chemotion ELN​

The Chemotion ELN’s data collector has to be configured to collect the mass spectrometer's data from the network location.

As for the file collector mechanism, there are two options.

  • Collecting attachment files from emails
  • Collecting file or folder from local drives or over SCP

For this procedure the folder collection from local drives or over SCP needs to be chosen and configured to collect the data from the network drive where the EFW program has uploaded it to.