Laboratoř Zobrazovacích Metod Viničná (VMCF)

Přírodovědecká Fakulta, Karlova Univerzita

Data Analysis

BioImage Analysis at Viničná Microscopy Core Facility

🚀 About Us

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.

🤝 What we offer

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

💡Bioimage Analysis Consultancy

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.

Arrange a Meeting

  • 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.

    Prepare for the Meeting

  • 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 😊

Image Data Preparation

  • 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
## 🖥️ Bioimage Analysis service
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.

Guidelines for a healthy cooperation

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.

💻 Available software

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

⌨️ Workstations

We plan to set up 3 new workstations that will be accessible through reservation system.

⚡High computing infrastructure

At the moment it is possible to use on-site server Mazlik, od to use BIOP-Desktop through onDemand service of metacentrum.

💾 Data storage

Please make yourself familiar with our Data Management Guidelines and Data Storage Guidelines.

🔬 Advanced imaging – available light microscopy equipment

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.

📖 Training

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.

Individual trainings

Courses and seminars

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.

You can check relevant university level classes and workshops we take part in.

👨‍💻 Our team

You can find dedicated page for contacts here.

💲Pricelist (without VAT)

Central price list is available zde.

📩 Contact

You can find us at:
Laboratoř Zobrazovacích Metod Viničná
Faculty of Science (Charles University)
Viničná 7
128 44 Prague 2
Česká Republika

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

🔗 More information and latest news