Syllabus & materials (2018)

This page contains the syllabus, lecture tittles & summaries & links to download course materials. Study materials include online references (follow the "useful links" on left side-bar), as well as the students' "technique assignments" (download from below).
For a really acessible intro to fluorescence microscopy and bioimage analysis I highly recommend Pete Brankhead's bookletFor medical imaging try Wikipedia. Don't forget that you will be able to study also from the individual student assignments, which can be downloaded when available. 

To download lecture slides, images for practicals and the individual student assignments follow this link.

List of lectures and practicals:

Lecture. Intro to bioimaging (G Martins 2.2.15)
General plan of the course. Distribution of individual student assignments and course programme details. What is Bioimaging? Review of important concepts.

Lectures. Principles of Light Microscopy and 3D microscopy (G Martins)
Light microscopy vs other imaging techniques. History of microscopy. Latest developments and trends. Fluorescence, resolution & the diffraction limit.
Spectral detection. The concept of 3D imaging. 3D microscopy techniques: confocals, multi-photon and mesoscopic techniques.

Lecture. Image capture & digital images in biology (G Martins)
Digital vs. analog. Image acquisition devices: CCDs vs CMOS cameras; PMTs;
High-speed cameras & time-lapse acquisition. 
 UV cameras, Thermography, Gamma & X-ray cameras.
Lecture. High-throughput microscopy & screening (H Botelho)
High-throughput imaging concepts and image based cytometry; Screening tools

Practical. Light microscopy & cams (@2.1.15; G Martins, + L Marques)
During this practical students will learn about optics and the following equipment: 
Fluorescence, filters, optics, lasers. Image capture. 
Microscope basics, widefield microscopy (fluorescence vs brightfield & contrasts); 
Digital image acquisition, noise & dynamic range.
Automated fluorescence stereoscope and time-lapse image acquisition;
Confocal microscopy and multidimensional image acquisition;
High-speed video acquisition with a "prosumer" camera & thermal imaging
For students interested there is an optional session for Scanning Electron Microcsopy.

Practical HTM demo (L Marques - FCUL C8)
In this demo the students will see a demonstration of a HTM high-throughout microscope and discuss the protocol for HTM imaging and screening. 

Practical. Advanced Microscopy Techniques  (Gaby, Nuno and Hugo @IGC)
Multi-photon vs confocal imaging. Components, principle and operation. 
Super-resolution, TIRF and spinningDisk confocal microscopy
Mesoscopy - Light-sheet and Optical Tomography; parts and operation. 

Lecture. Atomic Force Microscopy  (J Marquês 8.2.17)
            In this lecture students will learn about the principles of oepration of an AFM
            and types of images and imaging modes possible. 

Practical demo. AFM (J Marquês- FCUL 8.1.79) 
In this demo the students will see a demonstration of the AFM microscope @FCUL

Practical Advanced Microscopy techs (@IGC G Martins, N Martins, H Pereira) 
During this demo the students will see techniques such as spinning disk confocal, multi-photon, light-sheet, OPT and STORM/TIRF Super Resolution microscopy. 
This practical requires visiting the IGC - Instituto Gulbenkian de Ciencia in Oeiras. Here's how to get there

Lecture. Medical imaging/3D capture &  visualization (G Martins @2.3.13)
Radiography: X-rays use and detection. Fluoroscopy. Projectional vs tomographic images. CT ["TAC"] scanners. MicroCT (&MRI). Magnetic Resonance Imaging. 
Radiation sources in medical imaging, and nuclear medicine. Gamma cameras (Scintigraphy). PET - Positron Emission Tomography and SPECT. MRI - Virtual surgery and diagnostics. Ultrasonography (3D and 4D). In vivo (whole animal) molecular imagers. Thermal and NIR imaging in medicine.
3D image capture and visualization techniques in biology; The visible human project. 
Tomography and anatomical planes; Anatomical online databases. 

Lecture. PET Imaging (N Matela IBEB/FCUL  @2.3.13)

Practical demo. Medical MRI & CT imaging (HSM)
            During this demo the students will see the operation of medical MRI and CT scanners              at the Hospital Santa Maria (Max 16 students) Max 12 students

Practical demo. medical CT (IMAG - Olaias)
            During this demo the students will see the operation of a medical CT scanner at IMAG
            diagnsostics facility in Olaias.  
Requires visiting facility at Av.ª Afonso Costa, 41
            click here for address 
        Max 9 students

Practical demo. x-ray microCT (@IST; MF Pereira & A Mauricio) - March 1 16:00
During this demo the students will see the operation of an X-ray microCT system at IST geology museum, and acquisition of 3D images of juvenile fish cranium. 
The practical requires visiting "Pavilhão de Minas, Av. Rovisco Pais - saída metro saldanha nascente - Arco do cego, Museu de Mineralogia do IST"
Here's how to get there?             Max 10 students!
Encontro na entrada da Torre Sul de Química (entrada mais próxima junto à avenida Rovisco Pais). Prof Manuel Francisco estará no hall  da entrada junto à mesa de madeira grande para levar alunos ao museu no piso 3 do pavilhão de Minas. Espera até cerca das 16h15 e começa a visita! Telf do Lab: 218419295

Practical demo. microMRI (@CENIMAT FCT-UNL; P Almeida & M Corvo)
 - March2
            During this demo the students will see the operation of a microMRI system at 
            CENIMAT - FCT-UNL Caparica.
This practical requires visiting CENIMAT in Fac. Ciencias & Tecnologia, Almada.    Here's how to get to FCT  and once there, reach the CENIMAT here.
            Max 10 students!

Practical Demos 3D object scanner @MHNCUL, March 1st, 16:00
            During this demo the students will see the operation of a bench 3D scanner used for
            museum specimens. Requires visiting Museu de História Natural e Ciência at
Escola Politécnica. Directions here:

Practical. Image analysis exercises (2.3.16)
ImageJ for biologists. Installation and maintenance. 
Open images and obtain basic image information (metadata). ROIs. Histograms.
Saving and converting images types. 
Colors and image manipulation.
Analysing thermal images (grey density calibration) .  
Stacks and hyperstacks. 3D projections. 
Pixels to microns (pixel scaling). Image segmentation and measurements
Concept of bioimage analysis workflow/pipeline: process, enhance, segment & analyse. 
Correcting image defects (basic processing operations). 
Recording commands and re-applying (batch processing). 
Particle detection & analysis.
Analysing time-lapse sequences. Manual cell/particle tracking.
Measuring speeds and lags in high-speed movies.  Exporting as AVIs.
 3D rendering and colour-transfer functions in mic & medical images.
Discussion of ethics in image analysis and publication.
If time and pace permits we may discuss machine learning techniques.

(Exercises will use some images acquired during practicals + other examples. After the sessions, students should be able to carry out basic image processing and analysis techniques, extract numerical data and prepare images for publication with ImageJ.

List of 2017-2018 students & assignments

Click to => download student assignments

 NOME TurmaG  Tema individual (revisto!)
Catarina Pereira da Silva BBC 1 3D scanners in biology
Célia Domingues BBC 1 Noise in digital images & SNR
Francisco Santos BBC 1 CCD vs CMOS vs PMTs
Inês Vieira Oliveira BBC 1 Colocalization Analysis in mic
João Rebelo BBC 1 Digital images; bits, bytes, pixels & voxels
Paulo Nuno de Sousa BBC 2 image segmentation & particle analysis
Rita Isabel Dias Pacheco BBC 2 ImageJ/FIJI
Rui Sérgio de Sousa Luís BBC 2 PSF and deconvolution
Tânia Isabel Pina Santos BBC 2 High throughput/content screening mic
Vanessa Sofia Almeida BBC 2 Time-lapse, high-speed & video
Ana Catarina Gamado BED 3 GFP (& other FPs)
André Filipe Henriques BED 3 SpinningDisk confocal
Antelmo Alexandre Gonçalves BED 3 Super resolution in microscopy
Catarina Pires Rosa BED 3 Light-sheet microscopy
Francisco Manuel Bretes BED 3 Fluorescence+filters+dichroics
João Guilherme Frazão BED 3 Molecular imaging & biomarkers
Barbara Bairrão Ruivo BED 4 AFM - Atomic Force Microscopy
Mariana Bray Viegas BED 4 pre-clinical imaging
Paulo Miguel de Sousa BED 4 Multi-photon microscopy
Pedro Miguel dos Santos BED 4 Mouse Atlas project/Fishnet/Quail A Portal
Sara Cristina de Oliveira BED 4 Confocal microscopy
Tiago Charrua BED 4 Numerical aperture & resolution
Tiago Filipe Pereira BED 4 Optical projection tomography
Ana Catarina Pelicano EBB 5 PET medical imaging
Daniela Botnariuc EBB 5 Fluoroscopy
Filipa Diogo Silvestre EBB 5 MRI medical imaging
Filipe Miguel Dias Galvão EBB 5 SPECT imaging
Francisco Ruas Faro Viana EBB 6 CT medical imaging
Márcia Raquel de Abreu EBB 6 Thermography
Maria Francisca da Luz Canais EBB 6 Visible human project
Neusa Rebeca Adão Martins EBB 6 Ultrasonography