We are open access microscopy core facility, you can find as also at Laboratory of Confocal and Fluorescence Microscopy

Check out our Image Analysis and Data Processing in Super-Resolution Microscopy Workshop.

Consultation:

• Sample preparation
• Imaging
• BioImage Analysis

Services:

• Imaging
• BioImage Analysis
• User training

• Advanced Image analysis
• Image Analysis and Data Processing in Super-Resolution Microscopy (workshop)
• Molecular Probes
• Quantittive Microscopy

We provide variety of open access service, tailored fro specific of each projects:

• Consultations
  • Questions about where to search for software/plugins, which tools to choose for specific task. Learning about resources avilable. Consulting results, or already set up workflows.
  • Time scale: Hours to Days (depends on availability, check calendly)
• BioImage Analysis workflow setup
  • Design of workflow in specific tool/software. Seting up, or testing softwraes or tools. Preparing or re-running suplementary code from paper on users data.
  • Time scale: Days to weeks
• Pair programig development of BioImage Analysis tool
  • Colaborative development, rewriting or finetuning of BioImage Analysis tools.
  • Time scale: Weeks, months and more
• Running workflow/analysis for you
  • Time scale: depends on workflow
• Access to our presetup server with both open source and commercial BioImage Analysis tools

If you are not sure what to choose, short consultations is always best way to start.

• Any publications resulting from the use of tools within any facility should be acknowledged.
• If a particular member has provided significant help, expertise or generated additional data (including scripts, software or numeric results), they should be acknowledged by name and their personal contribution to the study.
• If scientist has rovided significant intellectual input, they should be co-authors.
• Co-authorship decisions should be made at the preparation stage of the manuscript. Co-authors reserves the right to review manuscripts containing results generated prior to submission.
• Each author should have made substantial contributions to the work, approved the submitted version, and agreed to be personally accountable for their own contributions and to ensure the accuracy and integrity of the work.
• The primary affiliation for each author should be the institution where the majority of their work was done, and if they have subsequently moved, the current address may also be stated.

We offer in person or online meetings.

Please book one of those slots in calendly.

You can also write a mail to <schatzm(at)natur.cuni.cz> describing in a few sentences what your question is about. We need this information to prepare.

It is extremly helpful to have two example images available; ideally already opened in FIJI such that we can inspect the raw data in detail together during the meeting; ideally the two images covering the range of phenomena you are investigating (e.g. positive and negative control).

Ideally, please also share some minimal example data with us. You can find detials in Image data preparation section.

If you can, it would be nice if you could prepare a short presentation, roughly following below suggestions. Of course, please modify this according to your project and leave out things that are not applicable. Please don't get stressed about preparing anything, we will help you in any case :)

• Slide 1: Scientific background
• Slide 2: Sample preparation and image acquisition
  • What's the specimen?
  • What kind of staining did you do?
  • Which microscope did you use?
• Slide 3: Example images
  • Ideally two images: treated and untreated with a visible difference of what should be measured
  • If above does not apply to your project it would still be nice if you could show more than one image such that we can get a feel for how variable the data is.
• Slide 4: Technicalities
  • Do you already know which number(s) you would like to measure?
  • How many images do you want to analyse (10,100,1000,10000,100000,...)?
  • How big are your individual images (MB, TB)?
  • Would you prefer a certain analysis software?
  • Do you already have experience with a certain analysis software?
  • Did you already try to analyse the data?

Best wishes and we looking forward to meeting you!

This document contains recommendations of how to organise your image data, e.g. when seeking consultancy at EMBL-CBA.

Select two (not more) images that ideally show a clear and biologically relevant difference.

For example the first image could be a control sample, whereas the second image has been treated in some way.

Please organise those two images into a folder structure similar to the one below:

• minimal-example-data
  • condition01
    • condition01_image01
  • condition02
    • condition02_image01
  • README.txt

As indicated please also add a short README text file where you describe in a few words what the difference is that you see between the conditions.

• High-end confocal microscope Leica TCS SP8 with one standard PMT and one sensitive HyD detector. Allows acquisition of fixed and living samples. The environmental chamber PECON with the CO2 regulation provides a suitable atmosphere for living cells experiments. The microscope offers several modes including lambda scanning, FRET and FRAP measurements, and is also equipped with a MATRIX module for object tracking during acquisition (e.g. growing oocytes or roots)

• The laboratory is equipped with a high-end inverted confocal microscope Leica TCS SP2 with AOBS (Acousto-Optical Beam Splitter) system, which ensures high sensitivity and the possibility to combine up to four fluorescence markers. The microscope allows structure analysis of fixed samples. It is possible to do multicolor analysis, 3D reconstructions, FRAP (Fluorescence Recovery After Photobleaching), FRET (Fluorescence Resonance Energy Transfer) analysis, and tile scans. There is a diode 405 nm laser installed.

• The most up-to-date confocal microscope Zeiss LSM 880 NLO is equipped with a set of lasers for one-photon excitation and with tunable Ti:Sa pulsed laser for two-photon excitation. High-sensitive 32-channel GaAsp spectral detector gets unrivaled clear images. It is possible to do one-channel FLIM (Fluorescence Lifetime IMaging), FCS (Fluorescence Correlation Spectroscopy), and RICS (Raster Image Correlation Microscopy) measurements which allow us to uncover molecular relationships and functions. The microscope works with high speed and high resolution. Live-cell imaging heated chamber with CO2 atmosphere is available as well.

• There is also a great wide-field system Olympus Scan^R available. It is equipped with a stabilized light source, high sensitive Hamamatsu camera, motorized stage, filter, and objective turrets and shutters. It is possible to do high-quality imaging as well as high throughput imaging and mosaic imaging. A high-quality stage chamber with the regulation of temperature (-5 to 65 °C) and gas level (CO2, O2) can maintain also multiwell dishes and allow high throughput imaging under different environmental conditions.

• Fully motorized fluorescence wide-field microscope NIKON TiE2 serves for fixed and living samples. It is equipped with a high-speed monochromatic ORCA Flash camera able to get 100 fps as well as with a nice RGB camera. Excitation Cool-LED P-4000 with 16 LEDs cover the full spectrum as well as SEDAT system of emission filters and multiband dichroic. OKOLab environmental chamber suits most common living cells demands. The microscope is driven by the full version of NIS-elements with High Content Imaging possibilities (JOBs module).

• A fully automated microscope ZEISS Axioscan Z.1 with the dock for 100 slides can easily and autonomously scan all of them at once. It is a workhorse for High Throughput Imaging of all of your tissue sections which could be reconstructed back to the 3D image of the sample.

• Microscope Zeiss Elyra PS.1 uses technologies of structured illumination (SIM) and precise localization (PALM/STORM) to overcome the so-called diffraction barrier, which limits us to the resolution of around 200 nm in conventional light microscopy. Nanoscopy allows us to observe structures with 2-3x higher resolution with SIM and up to 5 nm with localization microscopy. The microscope can use a technology of TIRF (Total Internal Reflection Fluorescence) to increase the signal-to-noise ratio in the space near to cover glass. A set of high-quality lasers and cameras help us to make great super-resolution images.

• Zeiss Lightsheet Z.1 microscope is great for rapid acquisition of fixed, living, or cleared samples in selective plane illumination. There are two pairs of 5x and 10x illumination objectives. Detection objective of 5x, 10x, 20x, and 40x and two objectives 20x for clearing RI 1.38 and 1.45. The chamber size is roughly 2x2x2 cm. The two-channel acquisition is driven by two cooled PCO cameras.