First-time users

The Imaging Facility at IEB (IFIEB) provides open access to its instrumentation and expertise for both internal and external users.

• Facility microscopes are self-operated, but training is mandatory before use.
  ⚠️ Unless specifically trained by the IFIEB staff, users are not allowed to operate any equipment.
• First, contact IFIEB staff to schedule an introductory training session.
• After training and understanding microscopy fundamentals (e.g., confocal microscopy basics), you will receive access to the online booking system and microscopes.
• External users request access via ifieb@ueb.cas.cz
• International external users are kindly requested to apply via the Euro-BioImaging access portal and when filling in the access proposal, click on the Czech Republic on the map and select “Advanced Light and Electron Microscopy Node Prague CZ” of which we are a part. More information about access via Euro-Bioimaging ERIC can be found here.

Support and training

IFIEB provides:

• User training and assisted sessions.
• Support with experimental design, sample preparation, and data acquisition.
• Help with or on demand data analysis (on request).

📌 IFIEB staff are here to help you and get the most of your imaging experiments — don’t hesitate to ask for assistance!

Booking a microscope

• All microscopes must be booked in advance via the reservation system (available here).
• Reservations are limited to 4 hours per user per day (9 AM–6 PM).
• Long-term time-lapse experiments must be scheduled outside peak hours (6 PM–9 AM or weekends).
• Cancel unused reservations in the booking system as early as possible. If other users are booked after or before your session, you might contact them so they can use the free time slot.

Usage rules

• Access is restricted to registered users only.
• Non-registered users may accompany a registered user but may not operate the microscope.
• Record each session in the logbook next to the microscope.

Report any issues or damages to facility staff and note them in the logbook.

• Handle microscopes with care, especially the objectives.
• Use only the correct immersion oil—never overapply oil or use it on air/water objectives.
• Avoid imaging at the slide/chamber edges to prevent objective scratching.
• Use only lens paper for cleaning objectives. To remove immersion oil, use Isopropanol (not technical ethanol).
• Follow the power-up and shutdown procedure as demonstrated by IFIEB staff.
• Never operate burners, lasers, or cameras without cooling devices.
• Leave the microscope and workspace clean after use.

🚨 Argon Lasers: If someone is scheduled after you, leave the laser in standby mode and confirm that they have started their session.

🔌 End-of-Day Users: Turn off the microscope system if you are the last user.

To ensure data integrity, accessibility, and reproducibility, follow these guidelines when saving and documenting your microscopy data.

Where to save your data?

🟢Preferred locations (backed up)

Save your data in one of the following locations (both are backed up):

• Imaging Facility Disc Station (\\ds-ueb-if.asuch.cas.cz\home)
• IEB P: drive (\\ds.asuch.cas.cz\home, 200GB capacity); recommended for short-term users

📌 Instructions for mapping these drives are available at each microscope.

🟠Temporary Storage (Not Backed Up)

• You may temporarily store data on the system’s DATA hard drive. Name your folder with your Surname (not First name only, please).
• Do not store the same data in both the DATA hard drive and the IF/IEB Disc Station.
• Delete your files from the DATA hard drive as soon as possible to free up space.

🔴Prohibited locations

Never save files on the computer’s desktop or C: drive—these files may be deleted without warning.

Data documentation

Every dataset you acquire must be accompanied by a README file to ensure future accessibility and reproducibility.

Why is the README file important?

• Ensures key details about the experiment are properly documented.
• Enables collaborators and facility staff to retrieve and understand and reuse your data.

Where to find the README template?

• Desktop folder of every microscope computer
• You can download the template here

What should your README file contain?

Include at least:

• Experiment details: Sample type, staining, microscopy settings, acquisition parameters (if not embedded in the file, or if relevant for the future analysis).
• File descriptions: What each file contains, naming conventions used.
• Processing steps (if any)
• Relevant metadata: If not embedded in the image files, include laser settings, exposure times, etc.
• Reference to your lab notebook: If more details exist in your lab notebook, include a note.
• License specifications, when needed.

• For publications

  • Deposit your datasets in a trusted repository (e.g. Zenodo, Figshare, Dryad, Bioimage Archive, the Czech Academy of Sciences repository (ASEP), or the Czech National Repository via CESNET/DataCite).
  • Ensure the repository of your choice issues a persistent identifier (DOI) and supports versioning of your dataset.
  • Provide complete metadata (data description, collection methods, file structure), include a recommended citation format, and attach an explicit license (e.g., CC-BY, CC-BY-NC, CC0 – see more information here).
  • In your manuscript, reference the DOI rather than asking readers to email you for data.

• For collaborations

  • Internal: UEB network file shares

  Our institution and the imaging facility provide access to backed-up storage that users can employ to share data within the users of the network.

  The Synology NAS drives allow setting user permissions for read/write access when sharing files and folders:

  • P: Drive (\lds.asuch.cas.cz\home) – 200GB per user, backed up.
  • Imaging facility disk station (\lds.ueb-if.asuch.cas.cz\home)
  • External – password-protected link is provided for data download

  • Internal and external

  • CESNET FileSender is ideal for one-time transfers up to 500GB, stored up to 1 month. You can login via eduID.cz federation and it allows for invitation to non-federated collaborators. Data is encrypted on the server and requires a decryption key for download.

  • Microsoft SharePoint (https://asuch-my.sharepoint.com) – allow for file version control.
  • General repositories like Zenodo or Figshare allow for restricted access to data, and have the advantage of providing a unique identifier. "

Prices in CZK per hour without VAT.

Reduced prices within CzechBioImaging access are possible via registration form access or by contacting IFIEB facility ifieb@ueb.cas.cz and must be followed by proper CzBI acknowledgement.

Zen black and Zen blue software

ZEN light

FiJi Software 

NIS Elements HASP driver

LasX 3.7.1 + Settings

NIS 5.3

Zen Blue 3.11

Zen Arivis Pro

SHE UTN Manager

Bioimage analysis

Bioimage book (Peter Bankhead): https://bioimagebook.github.io/index.html

Arivis Vision4D/ arivis Pro Knowledge hub: https://kb.arivis.com/vision4d-arivis-pro

Bioimage analysis python notebooks (Robert Haase): https://haesleinhuepf.github.io/BioImageAnalysisNotebooks/intro.html

iBiology - Bioimage analysis course: https://www.ibiology.org/online-biology-courses/bioimage-analysis-course/  

Microscopy, image acquisition

MATRIX – https://abberior.rocks/wp-content/uploads/8000_Matrix-2.pdf

Adaptive optics – https://abberior.rocks/wp-content/uploads/0242_adaptive_optics.pdf

Adaptive illumination – https://abberior.rocks/wp-content/uploads/0243_adaptive_illumination.pdf

Bioimaging guide: https://www.bioimagingguide.org/welcome.html

iBiology – Microscopy series: https://www.ibiology.org/online-biology-courses/microscopy-series/

Zeiss campus – Education in Microscopy and Digital imaging: https://zeiss-campus.magnet.fsu.edu/articles/basics/practical.html

Global bioimaging – Introduction to Confocal Microscopy: https://youtu.be/t6s9e6IofGE?si=RA7BxM_12KZkiA-3

Bioimaging community

Focal plane community site: https://focalplane.biologists.com/

Image.sc forum – software-oriented aspects of scientific imaging (e.g. image analysis, processing, acquisition, storage and management of digital scientific images): https://forum.image.sc/

Global bioimaging: https://globalbioimaging.org/

Euro bioimaging: https://www.eurobioimaging.eu/

Czech bioimaging: https://www.czech-bioimaging.cz/

GloBIAS – Global BioImage Analysts' Society: https://www.globias.org/home

CzechBIAS - Czech BioImage Analysts’ Society: https://czechbias.github.io/intro.html

QUAREP-LiMi - Quality Assessment and Reproducibility for Instruments & Images in Light Microscopy: https://quarep.org/

Acquisition, analysis and publishing guidelines

Aaron, J. and Chew, T.-L. (2021) A guide to accurate reporting in digital image processing – can anyone reproduce your quantitative analysis? Journal of Cell Science, 134. Available at: https://journals.biologists.com/jcs/article/134/6/jcs254151/237886/A-guide-to-accurate-reporting-in-digital-image.

Llopis, P.M., Senft, R.A., Ross-Elliott, T.J., et al. (2021) Best practices and tools for reporting reproducible fluorescence microscopy methods. Nature Methods, 18, 1463–1476. Available at: https://doi.org/10.1038/s41592-021-01156-w.

Waters, J.C. (2009) Accuracy and precision in quantitative fluorescence microscopy. The Journal of Cell Biology, 185, 1135–1148. Available at: https://rupress.org/jcb/article/185/7/1135/35453/Accuracy-and-precision-in-quantitative.

Senft, R.A., Diaz-Rohrer, B., Colarusso, P., et al. (2023) A biologist’s guide to planning and performing quantitative bioimaging experiments. PLoS Biology, 21, e3002167. Available at: https://journals.plos.org/plosbiology/article?id=10.1371/journal.pbio.3002167.

Schmied, C., Nelson, M.S., Avilov, S., et al. (2023) Community-developed checklists for publishing images and image analyses. Nature Methods, 21, 170–181. Available at: https://www.nature.com/articles/s41592-023-01987-9.