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Training and Microscopy Resources



We had previously contributed to teaching at the University of Cologne for bachelors', masters', and Ph.D. students on the topics of
  • Developmental Biology
  • Genetics
  • Evolution and Molecular Phylogenetics
  • Next generation sequencing of transcriptomes and genomes, comparative genomics
  • Image acquisition and processing
through various lectures, practicals, lab internships and rotations, and thesis projects (2008-2020).

Specific courses that we had been involved in (2012-2020) were:
  • Modern Techniques of Developmental Biology
    (MN-B-SM (DG 1), each semester, second half)
  • Advanced Light Microscopy
    (MN-B-SM (BG 2), summer semester, first half)
Current master's course offerings are described here. Complete student course offerings can be found through the Department's teaching pages. Note that these pages are mostly in German, with the exception of those for the Master's Degree, which is an international program taught in English.


Kristen has been the caretaker and has provided introductory training on the following systems:
  • DeltaVision RT inverted widefield fluorescence microscope (Applied Precision/ GE) and SoftWorx software for analysis and deconvolution (Biocenter Imaging Facility: Genetics building, rooms -1.M08 and -1.037a, which are across the corridor from each other). The analysis computer also has a license for Imaris v.5. Bookings for both the acquisition and analysis systems are made on-line through the Biocenter Imaging Facility.
  • Zeiss LSM700 confocal microscope (Biocenter room 3.201). Bookings are made on the calendar in the room.
  • General imaging advice for working with Zeiss microscopes (Biocenter room 3.507):
    • AxioImager.Z2 epifluorescent microscope with Apotome.2 module for structured illumination, with a motorized stage for high throughput, tiled acquisition
    • Lumar.V12 fluorescence stereomicroscope
    • AxioZoom.V16 fluorescence stereomicroscope
  • Light sheet microscopy (mDSLM model, Biocenter room 3.420). Our newest imaging system is supported by a wiki site that was developed by Maarten Hilbrant, including a user manual and hardware configurations (password protected access). Also check out his early work from attending the EMBO Light Sheet Microscopy Practical Course, hosted on the Openspim pages.
Contact Kristen by e-mail at kpanfili [at] to discuss how best to arrange any current training needs.


Page last updated 22 March 2021, K. Panfilio

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