i3S Imaging Platforms
The i3S node comprises five core facilities providing open-access to imaging technologies: Advanced Light Microscopy, Bioimaging, Biointerface and Nanotechnology, BioSciences Screening, and Histology and Electron Microscopy Scientific Platforms.
Together it enable multi-scale imaging from small animal models to nanostructures and allows the node to cover a wide range of research areas in biology and medical sciences, including cell biology, oncobiology, neurobiology, immunology, biomaterials, and nano- and regenerative medicine.
The node staff offers scientific advice on experimental design, training in the practical use of the equipment and image analysis, and scientific advice on developing research projects.
Moreover, we aim to advance knowledge in the field of bioimaging by offering postgraduate courses that will provide training in a range of techniques, including light microscopy, high-content imaging, atomic force microscopy, and image analysis.
Advanced Light Microscopy (ALM)
Bioimaging
Biointerfaces and Nanotechnologies (BN)
Biosciences Screening
Histology and Electron Microscopy (HEMS)
Advanced Light Microscopy
Advanced Light Microscopy (ALM) is the i3S scientific platform specializing in state-of-the-art optical microscopy for studying cellular systems in life science research areas such as cell biology, oncobiology, neurobiology, immunology, and biomaterials. The ALM provides open access to high-end imaging technology and extensive expertise in advanced optical microscopy applied to multi-dimensional imaging of cells and tissues, live cell imaging, functional and molecular imaging (e.g., FRAP, FRET, FLIM), and bio-image data analysis. Available equipment includes transmission/widefield fluorescence microscopes (one with TIRF), spinning disc microscopes (one with SR-SIM), laser scanning confocal microscopes (one with STED, FLIM, and FCS), and a light sheet microscope. Workstations with bio-image analysis software are also available.
The scientific platform provides scientific advice on experimental design, training in the practical use of equipment and image analysis, and scientific advice on the development of research projects. It also aims to increase knowledge in bioimaging by organizing several postgraduate courses in light microscopy and image analysis for the scientific and industrial communities.
The ALM is a core facility of the national PPBI-Portuguese Platform of BioImaging and the European research infrastructure Euro-Bioimaging ERIC.
3D Virtual visit (thanks to EUGLOHRIA European University Alliance for Global Health).
Resources
Equipment:
- Bruker Ultima 2Pplus
- Leica STELLARIS 8 STED FALCON
- Leica TCS SP8
- Leica TCS SP5II
- Nikon Crest X-Light V3 DeepSIM
- Andor BC43
- Andor Revolution XD
- ZEISS AxioImager Z1
- Leica DMI6000 FFW
- Leica DMI6000 Timelapse
- Nikon ECLIPSE Ti TIRF
- LEMOLish Lightsheet Fluorescence Microscope
- Digital Scanning Lightsheet Fluorescence Microscope
Software:
- CellProfiler
- QuPath
- Huygens
- Imaris
- MatLab
Offered Technologies
- Anisotropy/Polarization Microscopy
- Deconvolution Widefield Microscopy (DWM)
- Expansion microscopy
- Fluorescence Lifetime Imaging Microscopy (FLIM)
- Fluorescence Recovery After Photobleaching (FRAP)
- Förster Resonance Energy Transfer (FRET)
- High Performance Computational Cluster
- High Performance Workstation
- High Performance Workstation with high end GPU
- Intravital Microscopy (IVM)
- Laser Scanning Confocal Microscopy (LSCM/CLSM)
- Light-sheet Mesoscopic Imaging (SPIM or dSLSM)
- Photomanipulation
- Second/Third Harmonics Generation (SHG/THG)
- Spinning disk confocal microscopy (SDCM)
- Structured Ilumination Microscopy (SIM)
- Stimulated Emission Depletion Microscopy (STED)
- Fluorescence (Cross)-Correlation Spectroscopy (FCS/FCCS)
- Single Molecule Localization Microscopy (SMLM)
- Multiphoton Microscopy
- Widefield Microscopy
Publications
A list of publications, including work produced on the Advanced Light Microscopy Scientific Platform Resources (present-2012), can be found at ALM’s Zotero library
Job Shadowing
Bioimaging
We bring together a set of solutions for in vitro and in vivo imaging to advance in the development, improvement, integration, and use of bioimaging solutions through research, technology development, training and education with a focus on the fields of Biomaterials, Nano- and Regenerative Medicine in biology and medical science.
The Bioimaging operates on the basis of core projects and programmes at the bioimaging/biomaterials and/or regeneration interface. Resources available for imaging of biological events at different scales (molecular level, cellular level and small organism). We also provide support on project planning, experimental design, sample preparation, equipment operation, and image analysis.
Resources
Equipment:
- microCT SkyScan1276 (Bruker)
- Leica TCS SP5II
- Imaging flow cytometer (ImageStreamX, Cytek)
- ZEISS Axio Observer Z1
- Critical point dryer (CPD 7501, Polaron Range)
- Confocal Raman/FTIR Microscope, LabRAM HR800 UV, Horiba Jobin-Yvon
Software:
- CellProfiler
- CellProfiler Analyst
- Cytosplore
- ilastik
- MatLab
- QuPath
- R
- ZEISS ZEN
- CTAn (microCT, Bruker)
- CTVol (microCT, Bruker)
- CTVox (microCT, Bruker)
- DataViewer (microCT, Bruker)
- IDEAS (Imaging flow cytometry, ImageStream, Cytekl)
- LabSpec 5 (Confocal Raman/FTIR microspectroscopy)
- NRecon (microCT, Bruker)
Offered Technologies
- Fluorescence Recovery After Photobleaching (FRAP)
- Förster Resonance Energy Transfer (FRET)
- FTIR Spectroscopy
- Imaging Flow Cytometry
- Laser Scanning Confocal Microscopy (LSCM/CLSM)
- Raman Spectroscopy (RS)
- Microcomputed Tomography (microCT)
- Widefield Microscopy
- Sample preparation
Publications
- Freitas L, Bezerra A, Resende-Coelho A, Gomez-Lazaro M, Maciel L, Amorim T, Fernandes RJ, Fonseca H. Impact of Long-Term Swimming Exercise on Rat Femur Bone Quality. Biomedicines. 2023 Dec 22;12(1):35. doi: 10.3390/biomedicines12010035. PMID: 38255142; PMCID: PMC10813774.
- Rodrigues PM, Sousa LG, Perrod C, Maceiras AR, Ferreirinha P, Pombinho R, Romera-Cárdenas G, Gomez-Lazaro M, Senkara M, Pistolic J, Cabanes D, Klein L, Saftig P, Alves NL. LAMP2 regulates autophagy in the thymic epithelium and thymic stroma-dependent CD4 T cell development. Autophagy. 2023 Feb;19(2):426-439. doi: 10.1080/15548627.2022.2074105. Epub 2022 May 19. PMID: 35535798; PMCID: PMC9851248.
- Pinto R, Matula J, Gomez-Lazaro M, Sousa M, Lobo A, Zikmund T, Kaiser J, Gomes JR. High-resolution micro-CT for 3D infarct characterization and segmentation in mice stroke models. Sci Rep. 2022 Oct 19;12(1):17471. doi: 10.1038/s41598-022-21494-9. PMID: 36261475; PMCID: PMC9582034.
- Summers HD, Gomes CP, Varela-Moreira A, Spencer AP, Gomez-Lazaro M, Pêgo AP, Rees P. Data-Driven Modeling of the Cellular Pharmacokinetics of Degradable Chitosan-Based Nanoparticles. Nanomaterials (Basel). 2021 Oct 3;11(10):2606. doi: 10.3390/nano11102606. PMID: 34685047; PMCID: PMC8538870.
- Freitas A, Aroso M, Barros A, Fernández M, Conde-Sousa E, Leite M, Carvalho ED, Ribeiro CC, Ferreira R, Pêgo AP, Vitorino R, Gomez-Lazaro M. Characterization of the Striatal Extracellular Matrix in a Mouse Model of Parkinson’s Disease. Antioxidants (Basel). 2021 Jul 8;10(7):1095. doi: 10.3390/antiox10071095. PMID: 34356328; PMCID: PMC8301085.
- Freitas A, Aroso M, Rocha S, Ferreira R, Vitorino R, Gomez-Lazaro M. Bioinformatic analysis of the human brain extracellular matrix proteome in neurodegenerative disorders. Eur J Neurosci. 2021 Jun;53(12):4016-4033. doi:10.1111/ejn.15316. Epub 2021 Jun 16. PMID: 34013613.
Job Shadowing
- Training in non-so common technologies
- Microcomputed tomography
- Imaging flow cytometry
- Raman and FTIR microspectroscopy
Biointerfaces and Nanotechnologies
The Biointerfaces and Nanotechnology (BN) scientific platform combines fundamental and state-of-the-art technologies for the chemical, physical, and mechanical characterization of materials and biological samples at the macro-micro-nano level. We have expertise in the characterization of hydrogels, organoids, and tissue-based matrices (mechanical and rheological properties), functionalized surfaces (surface chemistry, morphology, wettability), and nanoparticles for diagnostics/therapeutics/theranostics (size, charge, ligand-receptor recognition) as well as other (bio)materials. Our goal is to contribute to excellence in modern materials research in health-related fields. We also have an educational mission by providing hands-on training to i3S users in the context of their research projects and by organizing undergraduate and postgraduate courses.
The i3S community, academia, and industry (nationally and internationally) have access to the equipment and expert staff support for a fee.
For more information on the techniques and equipment available, please call (+351 22 040 8800 Ext: 6057/ 5058), email (info.bn@i3s.up.pt), or follow this link. The BN Scientific platform is located in laboratory 004.S2.
Resources
Equipment:
- NanoWizard V, JPK/ Bruker
- Inverted fluorescence microscope (Observer Z7, ZEISS)
Software:
- JPKSPM Data processing (AFM NanoWizardV, JPK/ Bruker)
- JPKSPM software (AFM NanoWizardV, JPK/ Bruker)
- AtomicJ (AFM)
- Gwyddion (AFM)
- ZEISS ZEN
Offered Technologies
- Atomic Force Microscopy combined with Fluorescence Microscopy
Publications
- Moura RP, Carvalho ED, Martins C, des Rieux A, Pêgo AP, Sarmento B. Functionalized retinoic acid lipid nanocapsules promotes a two-front attack on inflammation and lack of demyelination on neurodegenerative disorders. J Control Release. 2023 Jun;358:43-58. doi: 10.1016/j.jconrel.2023.04.034. Epub 2023 Apr 28. PMID: 37088306.
- Moura D, Pereira AT, Ferreira HP, Barrias CC, Magalhães FD, Bergmeister H, Gonçalves IC. Poly(2-hydroxyethyl methacrylate) hydrogels containing graphene-based materials for blood-contacting applications: From soft inert to strong degradable material. Acta Biomater. 2023 Jul 1;164:253-268. doi: 10.1016/j.actbio.2023.04.031. Epub 2023 Apr 28. PMID: 37121371.
- Pereira AT, Rodrigues CRS, Silva AC, Vidal R, Ventura JO, Gonçalves IC, Pereira AM. Tailoring the Electron Trapping Effect of a Biocompatible Triboelectric Hydrogel by Graphene Oxide Incorporation towards Self-Powered Medical Electronics. ACS Biomater Sci Eng. 2023 Jun 12;9(6):3712-3722. doi: 10.1021/acsbiomaterials.2c01513. Epub 2023 May 31. PMID: 37256830; PMCID: PMC10265651.
- Timochenco L, Costa-Almeida R, Bogas D, Silva FALS, Silva J, Pereira A, Magalhães FD, Pinto AM. High-Yield Production of Nano-Lateral Size Graphene Oxide by High-Power Ultrasonication. Materials (Basel). 2021 Apr 12;14(8):1916. doi: 10.3390/ma14081916. PMID: 33921291; PMCID: PMC8069895.
- Silva FALS, Costa-Almeida R, Timochenco L, Amaral SI, Pinto S, Gonçalves IC, Fernandes JR, Magalhães FD, Sarmento B, Pinto AM. Graphene Oxide Topical Administration: Skin Permeability Studies. Materials (Basel). 2021 May 25;14(11):2810. doi: 10.3390/ma14112810. PMID: 34070414; PMCID: PMC8197561.
Job Shadowing
- Atomic force microscopy coupled to inverted fluorescence microscopy
BioSciences Screening
The BioSciences Screening platform offers advanced technology and expertise to tackle complex biological inquiries via high-throughput methods. Qualified scientists aid in project evaluation, assay development, and analysis, utilizing instruments like automated microscopy and microplate readers. We provide genetic and chemical screening with small animal and human cell-based models (2D, 3D), accessing extensive libraries for therapeutic discoveries.
The platform coordinates PT-OPENSCREEN (RNIE), accessing to compound synthesis/improvement and screening activities nationally. Additionally, it’s an EU-OPENSCREEN partner site for European drug discovery and contributes to the RNIE Portuguese Platform of BioImaging (PPBI) and COST actions.
Resources
Equipment:
- MultidropTM Combi Reagent Dispenser (Thermo-Scientific)
- JANUS with 4 Tip Arm and MDT Arm (PerkinElmer)
- Liquidator 96 (Metler-Toledo)
- ALPS 50 V-Manual Heat Sealer (Thermo-Scientific)
- Cell culture resources
- IN Cell Analyzer 2000 (GE Healthcare)
- Operetta CLS (Revvity)
- Opera Phenix Plus (Revvity)
- Synergy 2 (BioTek)
- SpectraMax iD3 (Molecular Devices)
- VICTOR Nivo (Revvity)
Software:
- Harmony 5.2
- Columbus Image Data Management and Analysis System
- CellProfiler
- CellProfiler Analyst
- shinyHTM
- Spotfire
Offered Technologies
- High Throughput Microscopy/High Content Sreening (HTM/HCS)
- High Performance Computational Cluster
- Sample preparation
Publications
- Maia, A. F. and Gomez-Lazaro, M. (2021). High-content microscopy. In Imaging Modalities for Biological and Preclinical Research: A Compendium (ed. Walter, A.), Mannheim, J.), and Caruana, C.), p. I.1.d-1-14. Institute of Physics Publishing.
- Pinto, M. F., Figueiredo, F., Silva, A., Pombinho, A. R., Pereira, P. J. B., Macedo-Ribeiro, S., Rocha, F. and Martins, P. M. (2021). Major Improvements in Robustness and Efficiency during the Screening of Novel Enzyme Effectors by the 3-Point Kinetics Assay. SLAS discovery?: advancing life sciences R & D 26, 373–382.
- Ferreira, J. R., Teixeira, G. Q., Neto, E., Ribeiro-Machado, C., Silva, A. M., Caldeira, J., Leite Pereira, C., Bidarra, S., Maia, A. F., Lamghari, M., et al. (2021). IL-1β-pre-conditioned mesenchymal stem/stromal cells’ secretome modulates the inflammatory response and aggrecan deposition in intervertebral disc. European cells & materials 41, 431–453.
- Fernandes, A. S., Pombinho, A., Teixeira-Duarte, C. M., Morais-Cabral, J. H. and Harley, C. A. (2021). Fluorometric Liposome Screen for Inhibitors of a Physiologically Important Bacterial Ion Channel. Frontiers in microbiology 12, 603700.
- Biselli, S., Alencastre, I., Tropmann, K., Erdmann, D., Chen, M., Littmann, T., Maia, A. F., Gomez-Lazaro, M., Tanaka, M., Ozawa, T., et al. (2020). Fluorescent H2 Receptor Squaramide-Type Antagonists: Synthesis, Characterization, and Applications. ACS medicinal chemistry letters 11, 1521–1528.
- Henriques, P. C., Costa, L. M., Seabra, C. L., Antunes, B., Silva-Carvalho, R., Junqueira-Neto, S., Maia, A. F., Oliveira, P., Magalhães, A., Reis, C. A., et al. (2020). Orally administrated chitosan microspheres bind Helicobacter pylori and decrease gastric infection in mice. Acta biomaterialia.
- Pádua, D., Barros, R., Amaral, A. L., Mesquita, P., Freire, A. F., Sousa, M., Maia, A. F., Caiado, I., Fernandes, H.,Pombinho, A., et al. (2020). A SOX2 Reporter System Identifies Gastric Cancer Stem-Like Cells Sensitive to Monensin. Cancers 12,.
- Gomes, R. N., Borges, I., Pereira, A. T., Maia, A. F., Pestana, M., Magalhães, F. D., Pinto, A. M. and Gonçalves, I. C. (2018). Antimicrobial graphene nanoplatelets coatings for silicone catheters. Carbon.
- Palha, A. M., Pereira, S. S., Costa, M. M., Morais, T., Maia, A. F., Guimarães, M., Nora, M. and Monteiro, M. P. (2018). Differential GIP/GLP-1 intestinal cell distribution in diabetics’ yields distinctive rearrangements depending on Roux-en-Y biliopancreatic limb length. Journal of Cellular Biochemistry 46, 1954.
- Rocha, H., Maia, A. F. and Gassmann, R. (2018). A genome-scale RNAi screen for genetic interactors of the dynein co-factor nud-2 in Caenorhabditis elegans. Scientific Data 5, 180047– 8.
Job Shadowing
- In the context of the scientific platform daily work we provide training and assistance to all the users of the equipment.
Histology and Electron Microscopy
The Histology and Electron Microscopy platform is focused on Electronic Microscopy (EM), namely sample preparation; conventional ultrastructural analysis in 2D; immunogold-labeling; negative staining ; elemental analysis – energy-dispersive X-ray spectroscopy (STEM-EDS), and Optical Microscopy (OM) namely grossing, processing, embedding and sectioning; special stains; cryoprocessing and immunohistochemistry. The Histopathology service, within HEMS offers a full range of macroscopic and histopathology services, able to support research groups using animal models or human tissues in histopathology studies. The unit provides the equipment, technical support and guidelines to
researchers needing high level electron and optical microscopy to tackle studies either of cells, tissues or material sciences, not only for i3S and the University of Porto, but also outside institutions for industry and companies’ users. HEMS can help to define optimal experimental conditions for the research as wells to participate in the projects. Besides the training courses for researchers, masters and PhD programmes, the unit also offers internships for higher education students. Currently, the unit is engaged in workshops or exhibitions for the general public organised by the i3S Communication Unit.
Resources
Equipment:
- Cryostat epredia – NX50 IQOQ
- Cryostat Leica CM 3050S
- Paraffin tissue processor
- Microm Modular embedding system
- Microm Paraffin microtome
- Microm HM335E Paraffin
- Vibratome – LEICA VT 1200S
- Tissue Chopper McILwain EC350
- Brightfield Microscope – Leica DM2000 LED
- Brightfield Microscope – Olympus DP 25 Camera Software Cell B
- Ventana Discovery Ultra Platform (Roche)
- PhenoimagerTM HT (Akoya Biosciences)
- Hyperion Tissue Imaging System (CyTOF system, Standard Biotools)
- Transmission Electron Microscope Jeol JEM 1400
- STEM detector and EDS system
- Scanning Electron Microscope – Phenom XL
- Sputter coater / Glow Discharge – Leica EM ACE200
- Ultramicrotome Leica Reichert SuperNova
- Ultramicrotome PT RMC RMC PowerTome PC=XL
- Knifemaker Leica Glass
Software:
Offered Technologies
- Grossing & Processing & Embedding & Sectioning
- H&E staining
- Cryosectioning
- Tissue sections for DNA extraction
- Histogel processing
- Immunohistochemistry and immunofluorescence (simple or multiplexed)
- Digital scanning (brightfield and fluorescence)
- Imaging Mass Cytometry (IMC) (CyTOF)
- Histology image analysis
- Conventional ultrastructure
- Immunoelectromicroscopy
- Negative and cytochemistry stains
- Energy Dispersive X-ray Spectrometry (EDS)
- Consultation in tissue analysis.
- Scanning Electron Microscopy (SEM)
- Transmission Electron Microscopy (TEM)
- Widefield Microscopy
- Sample preparation
Publications
- Ferreira D, Santos-Pereira C, Costa M, Afonso J, Yang S, Hensel J, McAndrews KM, Longatto-Filho A, Fernandes R, Melo JB, Baltazar F, Moreira JN, Kalluri R, Rodrigues LR. Exosomes modified with anti-MEK1 siRNA lead to an effective silencing of triple negative breast cancer cells. Biomater Adv. 2023 Nov;154:213643. doi: 10.1016/j.bioadv.2023.213643. Epub 2023 Sep 28. PMID: 37778291.
- Rocha DN, Carvalho ED, Pires LR, Gardin C, Zanolla I, Szewczyk PK, Machado C, Fernandes R, Stachewicz U, Zavan B, Relvas JB, Pêgo AP. It takes two to remyelinate: A bioengineered platform to study astrocyte-oligodendrocyte crosstalk and potential therapeutic targets in remyelination. Biomater Adv. 2023 Aug;151:213429. doi: 10.1016/j.bioadv.2023.213429. Epub 2023 Apr 25. PMID: 37148597.
- Báo SN, Machado M, Da Silva AL, Melo A, Cunha S, Sousa SS, Malheiro AR, Fernandes R, Leite JRSA, Vasconcelos AG, Relvas J, Pintado M. Potential Biological Properties of Lycopene in a Self-Emulsifying Drug Delivery System. Molecules. 2023 Jan 26;28(3):1219. doi: 10.3390/molecules28031219. PMID: 36770886; PMCID: PMC9920511.
- Catarina Moreira-Barbosa, Andreia Matos, Rui Fernandes, Miguel Mendes-Ferreira, Rafaela Rodrigues, Tânia Cruz, Ângela Margarida Costa, Ana Patrícia Cardoso, Carmen Ghilardi, Maria José Oliveira, Ricardo Ribeiro, Chapter 5 – The role of fatty acids metabolism on cancer progression and therapeutics development, Bioactive Lipids, Academic Press, 2023, Pages 101-132.
- Sousa A, Rufino AT, Fernandes R, Malheiro A, Carvalho F, Fernandes E, Freitas M. Silver nanoparticles exert toxic effects in human monocytes and macrophages associated with the disruption of Δψm and release of pro-inflammatory cytokines. Arch Toxicol. 2023 Feb;97(2):405-420. doi: 10.1007/s00204-022-03415-x. Epub 2022 Nov 24. PMID: 36424514.
- Stevanović-Silva J, Beleza J, Coxito P, Rocha H, Gaspar TB, Gärtner F, Correia R, Fernandes R, Oliveira PJ, Ascensão A, Magalhães J. Exercise performed during pregnancy positively modulates liver metabolism and promotes mitochondrial biogenesis of female offspring in a rat model of diet-induced gestational diabetes. Biochim Biophys Acta Mol Basis Dis. 2022 Nov 1;1868(11):166526. doi: 10.1016/j.bbadis.2022.166526. Epub 2022 Aug 20. PMID: 35995315.
- Morais M, Machado V, Dias F, Figueiredo P, Palmeira C, Martins G, Fernandes R, Malheiro AR, Mikkonen KS, Teixeira AL, Medeiros R. Glucose-Functionalized Silver Nanoparticles as a Potential New Therapy Agent Targeting Hormone-Resistant Prostate Cancer cells. Int J Nanomedicine. 2022 Sep 16;17:4321-4337. doi: 10.2147/IJN.S364862. PMID: 36147546; PMCID: PMC9489222.
- Baptista-Silva S, Bernardes BG, Borges S, Rodrigues I, Fernandes R, Gomes-Guerreiro S, Pinto MT, Pintado M, Soares R, Costa R, Oliveira AL. Exploring Silk Sericin for Diabetic Wounds: An In Situ-Forming Hydrogel to Protect against Oxidative Stress and Improve Tissue Healing and Regeneration. Biomolecules. 2022 Jun 8;12(6):801. doi: 10.3390/biom12060801. PMID: 35740928; PMCID: PMC9221298.
- Cruz AF, Fonseca NA, Malheiro AR, B Melo J, Gaspar MM, Fernandes R, Moura V, Simões S, Moreira JN. Targeted liposomal doxorubicin/ceramides combinations: The importance to assess the nature of drug interaction beyond bulk tumor cells. Eur J Pharm Biopharm. 2022 Mar;172:61-77. doi: 10.1016/j.ejpb.2022.01.006. Epub 2022 Jan 31. PMID: 35104605.
- de Sousa A, AbdElgawad H, Fidalgo F, Teixeira J, Matos M, Tamagnini P, Fernandes R, Figueiredo F, Azenha M, Teles LO, Korany SM, Alsherif EA, Selim S, Beemster GTS, Asard H. Subcellular compartmentalization of aluminum reduced its hazardous impact on rye photosynthesis. Environ Pollut. 2022 Dec 15;315:120313. doi: 10.1016/j.envpol.2022.120313. Epub 2022 Oct 11. PMID: 36228849.
Job Shadowing