Welcome to the Viničná Microscopy Core Facility! We are an open-access resource specializing in advanced microscopy and bioimage analysis. As part of the Laboratory of Confocal and Fluorescence Microscopy, we offer a wide range of services, including cutting-edge imaging technologies and expert analytical support to meet your research needs.

Our Mission: To offer consistent, high-quality microscopy and bioimage analysis services, enabling reproducible and impactful scientific research.

Consultations	Services	Teaching
Sample preparation Imaging techniques Bioimage analysis	Advanced imaging Bioimage analysis Software and infrastructure access User training	Personalized training Workshops and group courses

Our Image Analysis Consultancy provides personalized support to help you optimize and navigate your bioimage analysis workflows. Whether you're establishing new processes or refining existing ones, we're here to assist every step of the way.

• Booking: Schedule an in-person or online meeting by selecting a slot through Calendly or by emailing us with a brief description of your inquiry. This helps us prepare effectively for your session.

• Necessary Preparation: Select two (not more❗) example images, ideally opened in FIJI, so we can inspect the raw data in detail during the meeting. Choose images that represent the range of phenomena you're investigating (e.g., positive and negative controls).
• (Optional) Data Sharing: Sharing a minimal set of example data in advance can be very helpful. Details on data preparation can be found in the "Image Data Preparation" section below.
• (Optional) Presentation: If possible, prepare a short presentation covering the following topics:
  • Scientific Background: An overview of the project.
  • Sample Preparation and Image Acquisition: Details on the specimen, staining methods, and microscopy used.
  • Example Images: Ideally, provide treated and untreated images that show a clear difference. If not applicable, show a range of images to illustrate data variability.
  • Technical Details: Clarify the specific numbers you wish to measure, the volume of data (e.g., 10, 100, 1,000 images), image sizes, preferred software, and any preliminary analysis attempts.

Don't be stressed, if you're unsure what to bring, just come to us, we will help you 😊

• Organize Your Data: Select a minimal set of representative images that clearly show biologically relevant differences.
• Suggested Folder Structure:

  minimal-example-data/
  ├── condition01/
  │   └── condition01_image01.tif
  ├── condition02/
  │   └── condition02_image01.tif
  └── README.txt
  

Our facility offers a wide range of open-access services designed to meet the unique requirements of your bioimaging projects. Whether you need assistance with image analysis, workflow setup, or custom tool development, our team is here to support you.

We provide expert consultations and training, and can develop tailored image analysis workflows to fit your specific scientific goals. Our infrastructure, equipped with cutting-edge workstations, High Performance Computing, and a variety of bioimage analysis tools, allows for remote access and seamless data handling from anywhere.

In line with the principles of open science, we adhere to the FAIR guidelines, ensuring that our services and solutions promote data transparency, accessibility, and reusability.

• Consultations:

  • Get help choosing the right software, plugins, and tools for your tasks.
  • Find resources and get advice on interpreting results or improving your workflows.
  • Timeframe: Few hours to a few days (depending on availability; check our Calendly for booking).

• Workflow Setup:

  • Design and set up analysis workflows tailored to your needs.
  • We can help with software setup, testing, and running code from published papers using your data.
  • Timeframe: Few days to a few weeks.

• Pair Programming for Tool Development:

  • Work with us to develop, refine, or improve BioImage Analysis tools through collaborative programming.
  • Timeframe: Usually takes several weeks to months, depending on the project.

• Workflow Execution:

  • We can run analysis workflows for you on our server, which has both open-source and commercial BioImage Analysis tools.
  • Timeframe: Varies depending on the complexity of the workflow.

If you're unsure where to start, we recommend scheduling a short consultation to discuss your needs and determine the best approach.

To ensure a smooth and productive partnership, please consider the following guidelines when publishing results derived from our collaboration:

• Acknowledgment: Any publications resulting from the use of our tools or services should include an acknowledgment of the facility.
• Authorship: If a team member provided significant intellectual input or contributed additional data (e.g., scripts, software, or numerical results), they should be acknowledged by name or considered for co-authorship.
  • Co-Authorship: Co-authorship decisions should be made during the manuscript preparation stage. Co-authors reserve the right to review any manuscript containing results generated by the facility before submission.
  • Contributions: Each author should have made substantial contributions to the work, approved the final version, and agreed to be accountable for their contributions to ensure the accuracy and integrity of the research.
  • Affiliations: The primary affiliation for each author should be the institution where the majority of their work was conducted. If the author has since moved, their current address may also be included.

	ZEISS Arivis Pro		ZEISS ZEN
	SVI Huygens Professional		NIS Elements
	SPCImage FLIM analysis		BIOP-Desktop
	ImageJ/FIJI		Napari
	Cellpose		Ilastik
	QuPath		and more...

At our core facility, we offer advanced microscopy techniques, including super-resolution, confocal, and high-throughput imaging. Our team is here to help you select the best tools and fine-tune your workflows, ensuring you get the most valuable insights from your samples.

Our core facility offers a variety of training options that are tailored to meet the unique needs of our users. Whether you're a seasoned microscopist looking to improve your workflow or a first-time user, we have courses and workshops specifically designed for you.

• User-defined training sessions
• How to: BIOP-Desktop in Metacentrum OnDemand
• How to: Jupyter Hub

Our courses, seminars, and workshops are designed to provide an in-depth understanding of bioimage analysis, with a focus on practical applications for interpreting microscopy data.

• 4EU+ Advanced Image analysis
• 4EU+ Molecular Probes in Biomedical Imaging
• 4EU+ Quantitative Microscopy
• Image Analysis and Data Processing in Super-Resolution Microscopy (workshop)
• Fundamentals of bioimage analysis (workshop)

	Martin Schätz Email: martin.Schatz@natur.cuni.cz, X: @SchatzCz, ORCID:0000-0003-0931-4017 Specializes in designing and implementing advanced workflows for user projects, advising on experimental design, and managing research data. His work includes teaching advanced image analysis techniques, research data management, open science and mentoring researchers on microscopy and data processing.
	Judith Garcia-Gonzalez Email: garciagj@natur.cuni.cz, X: @judith_garciago Specializes in bioimage analysis with expertise in cell and cytoskeleton segmentation, and has extensive experience in studying protein dynamics and interactions using fluorescence microscopy. Her work also includes teaching both foundational and advanced bioimage analysis techniques.
	Team member Email: team_member@natur.cuni.cz, X: @team_member Team member description

You can find us at:
Viničná Microscopy Core Facility
Faculty of Science (Charles University)
Viničná 7
128 44 Prague 2
Czech Republic

For any inquiries or to schedule a consultation, please reach out through the following:

• Email: konfmi@natur.cuni.cz
• Schedule a Meeting: Calendly
• Consultancy Guidelines: Please review the Bioimage Analysis Consultancy section before booking a consultation.

  VMCF GitHub
  X (@IMCF_vinicna)
  Viničná Microscopy Core Facility (VMCF)
  Laboratory of Confocal and Fluorescence Microscopy (KONFMI)