Czech-Bioimaging Activities of CBIA

Since 2016, CBIA is a part of the national research infrastructure for biological and medical imaging (Czech-BioImaging, part of Euro-BioImaging), which is a distributed infrastructure of leading imaging facilities in the Czech Republic. The infrastructure provides an open access to a wide range of imaging technologies and expertise to all scientists in the Czech Republic and from abroad.

What we Offer

The main role of CBIA in this consortium is to provide open access to a wide range of biomedical image analysis resources and services. For this purpose, CBIA is well equipped with state-of-the-art big data computational and data storage equipment and the CBIA staff has a broad experience in the field. The focus is thus on creating tailor-made solutions for difficult image analysis problems that biologists or physicians need to solve and that cannot be addressed using commercially available or open-access solutions. These difficult biomedical image analysis tasks are solved in the frame of common long-term projects financed from Czech-Bioimaging as well as other sources. We also provide unique (on international level) benchmarking resources (especially for cell imaging) supplemented by educational activities (courses, summer schools, tutorials at ISBI and MICCAI conferences, etc.).

Secondarily, we also provide open access to selected automated microscopy techniques, especially we focus on automated confocal spinning disk microscopy. We offer the following two setups:

• Location: Faculty of Informatics, Room A316
• Microscope: inverted Olympus IX83
• Objectives: 10x/NA0.4, 20x/NA0.75, 20x/NA0.5/PhC, 40x/NA0.75/PhC, 40x/NA1.15/Water
• Confocal unit: Yokogawa CSU-W1 with quad-band dichroic mirror and motorized bypass
• Camera: Andor iXon-Ultra-888 back-illuminated 1024x1024 EMCCD at -80°C
• X-Y movement: Märzhäuser SCAN-IM stage (stepper motors)
• Z movement: Märzhäuser Piezo Z-Stage 300μm + internal stepper motor
• Filter exchange (wide-field mode): internal filter-cube revolver (DAPI/FITC/Cy3/Cy5)
• Filter exchange (confocal mode): filter wheel inside confocal (DAPI/FITC/Cy3/Cy5/quad)
• Light source (wide-field mode): external X-Cite 120W lamp
• Light source (confocal mode): VisiTech Laser Combiner with 4 solid state lasers (405/488/561/640nm at 120/100/100/150mW, respectively)
• Live cell chamber: Ökolab H301-MINI chamber with temperature, CO2 and humidity control
• Anti-vibration base: Thorlabs breadboard

• Location: Bohunice Campus, Room A3/2.23
• Microscope: inverted Zeiss Axiovert 200M
• Objectives: 10x/NA0.3, 20x/NA0.5/PhC, 40x/NA0.75, 40x/NA1.3/Oil, 63x/NA1.3/Water, 100x/NA1.45/Oil
• Confocal unit: Yokogawa CSU-10 with quad-band dichroic mirror
• Camera (wide-field mode): Photometrics CoolSNAP HQ2 1392x1040 CCD at -30°C
• Camera (confocal mode): Andor iXon+ 888 back-illuminated 1024x1024 EMCCD at -80°C
• X-Y movement: Prior inverted ProScan H117 stage (stepper motors)
• Z movement: Prior 500μm NanoScanZ piezo + internal stepper motor
• Filter exchange (wide-field mode): internal filter-cube revolver (DAPI/FITC/Cy3/Cy5)
• Filter exchange (confocal mode): Sutter Lambda 10-3 filter wheels (DAPI/FITC/Cy3/Cy5/quad)
• Light source (wide-field mode): external X-Cite 120W lamp
• Light source (confocal mode): Andor Laser Combiner LC-401A with 4 solid state lasers (405/488/561/640nm at 50/75/75/40mW, respectively)
• Live cell chamber: Lab-Tek mini-chamber with pre-mixed CO2 supply and temperature control
• Anti-vibration base: Thorlabs breadboard

How to Apply

If you are interested in our services, please contact Michal Kozubek to discuss your problem and to find a suitable collaboration scheme. Typically, sample image data need to be supplied or acquired and a common (usually long-term) project defined afterwards. A short project proposal must be then submitted using a Czech-Bioimaging application form.

Acknowledgment

Our Czech-BioImaging activities are supported from the program for large research infrastructures of the Ministry of Education, Youth and Sports (MEYS) of the Czech Republic (Projects LM2023050 and CZ.02.1.01/0.0/0.0/18_046/0016045). Please acknowledge CBIA and our funding in your publications and other outputs when using our services. The preferred wording is: "We acknowledge the Centre for Biomedical Image Analysis at Masaryk University supported by MEYS CR (LM2023050 and CZ.02.1.01/0.0/0.0/18_046/0016045 Czech-BioImaging) for their support with obtaining scientific data presented in this paper." Alternatively, you can specify more precisely what kind of help was provided instead of „obtaining scientific data“.