How to cite the use of Huygens in scientific papers.
Good scientific practice demands that experiments can be repeated. Thus, when perpforming an experiment and publishing a scientific paper or book chapter, you should describe how microscopy images were acquired, restored, and analyzed. If the parameters automatically estimated by Huygens were not adjusted, it is sufficient to only describe the Huygens tool and version number used. Below are a few examples of how you can refer to the use of Huygens.
Huygens Essential 25.10 was used to correct crosstalk using the estimated values, and to perform deconvolution with the "Standard" Deconvolution Express strategy (Scientific Volume Imaging, The Netherlands). The deconvolved results were subjected to object geometry and intensity measurements with Huygens Object Analyzer with Threshold and Seed values set to 14 and 10%, respectively.
All widefield and confocal images were deconvolved on-the-fly with Huygens Batch Feeder version 25.10 using the " Standard" strategy (Scientific Volume Imaging, The Netherlands, http://svi.nl). Maximum Intensity Projections were generated with the Slicer with gamma settings as described in the figure legends. Nuclei were counted using AI-based analysis within Huygens Object Analyzer with minimum size set to 4 microns and default threshold setting.
For improved accuracy of colocalization measurements, all spinning disk data were deconvolved and corrected for chromatic aberration. For this we used batch processing with pre-made templates within the Workflow Processor in Huygens Professional (version 24.10). The template for deconvolution included default settings and CMLE algorithm, Acuity: -5.3, SNR:20, 40 iterations, and background value on Auto. A template for chromatic aberration was created by estimating the shift and rotating parameters within a 170nm multichannel bead image aquired using similar microscopy settings.
You may consider to include with a publication the Huygens templates and log files, which include the applied restoration and analysis parameters.
Once your paper has been accepted, we would be very happy to post a link to your publication on our website. You can submit a reference to your paper via this Submit References form.