Microscopes, Software, and Computing Capacity

Revvity Opera Phenix PLUS includes:

• Spinning-disk confocal
• Imaging in confocal, widefield, digital phase contrast, brightfield and AI brightfield modes
• 5 lasers: 405nm, 425nm, 488nm, 561nm, and 640nm
• Emission filters
• 7 objectives
  • 4 long working distance air objectives: 5x NA 0.16, 10x NA 0.3, 20x NA 0.4, 40x NA 0.6
  • 3 water immersion objectives: 20x NA 1.0, 40x NA 1.1, 63x NA 1.15
• 4 Andor Zyla sCMOS cameras, 2160x2160 pixels (6.5um pixel size)
• Environmental control for live cell imaging
  • Temperature control 30-45 oC with 1 oC increments
  • CO2 control 1-10% with 0.5% increments
  • Humidity controls
• Various multi-well plates supported, and a slide holder for up to 4 slides
• Plate Handler Flex automation for 66 plate positions in RT
• Liconic incubator with 44 plate positions for automated live cell imaging experiments
• (Same automation system integrated with PerkinElmer Opera Phenix High Content Screening System )

PerkinElmer Opera Phenix includes:

• Spinning-disk confocal
• Imaging in confocal, widefield, digital phase contrast and brightfield modes
• 4 lasers: 405nm, 488nm, 561nm, and 640nm
• 7 objectives
  • 4 long working distance air objectives: 5x NA 0.16, 10x NA 0.3, 20x NA 0.4, 40x NA 0.6
  • 3 water immersion objectives: 20x NA 1.0, 40x NA 1.1, 63x NA 1.15
• 2 Andor Zyla sCMOS cameras, 2160x2160 pixels (6.5um pixel size)
• Environmental control for live cell imaging
  • Temperature control 37-42 oC with 1 oC increments
  • CO2 control 1-10% with 0.5% increments
• Various multi-well plates supported, and a slide holder for up to 4 slides
• Plate Handler Flex automation for 66 plate positions in RT
• Liconic incubator with 44 plate positions for automated live cell imaging experiments

• High-throughput microscope with four PlanApo and PlanFluor objectives; 4x, 10x, 20x and 40x magnifications. Environment control for temperature, humidity and CO2 for live imaging
• Imaging in widefield, digital phase contrast and brightfield modes with band-pass filters for DAPI, FITC, TRITC, TexasRed and Cy5 emmision ranges
• Various multi-well plates supported, and a slide holder for up to 3 slides at a time

Leica LMD7 Laser microdissection system

The system comprises a Leica LMD7 inverted widefield microscope with long working distance objective lenses (10x, 20x, 40x, 63x). The microscope has filters for TRITC, FITC and DAPI wavelenghts. The system uses LAS X software for imaging and basic analysis. Computer Assisted Microscope Imaging (CAMI) pipeline uses the SCT BIAS software package, which can utilize any set of image data from either FIMM-HCA equipment or from a variety of other microscope systems with three calibration points visible in the sample. BIAS is used for deep learning based image analysis, cell classification and contour export of single cells or tissue areas from membrane slides for microdissection in the LMD7. Dissected samples can then be processed and analyzed with methods such as single cell sequencing (in collaboration with ) or proteomics.

Computing workstations

We provide two workstations for users for their data management and image analysis needs available through Openiris. HCA1 located in Biomedicum 2U (FIMM), D206a2 and HCA3 located in Biomedicum 2U (FIMM), D204b. You can also access them through Anydesk application from home or office. ask our for the access details. 

HCI1 proprietary software installed:

• 5.2, compatible with the PerkinElmer Opera Phenix microscope (Data management and image analysis)
• Biological image analysis software (Image analysis and contour export for LMD)
• for signals one (Data analysis, exploration and visualization)

HCI3 (Lenovo Thinkstation P3 Tower gen2, CPU: Intel core Ultra 9, GPU: NVIDIA RTX 5000 Ada 32Gb) proprietary software installed:

• 5.3, compatible with the Revvity Opera Phenix PLUS (Data management and image analysis)
• Biological image analysis software (Image analysis and contour export for LMD)
• for signals one (Data analysis, exploration and visualization)

Data management and software

Secure data server for image storage for up to 6 months (regular service) or upon agreement. >300 TB of storage for all users. Data will be archived on lsdcc servers, which can be accessed from any computer with the university VPN connection upon request.