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Facultad de Medicina

2º Image Analysis in Biomedical Research Course

Date and Place

4th-8th March 2019 (15:00-19:00h).

Seminario 7. Facultad de Medicina
Universidad Autónoma de Madrid.
C/Arzobispo Morcillo 4. 28029 Madrid

Summary and objectives. Biomedical research often uses techniques that require image analysis (Western blot, measurements of biomolecules, morphometric analysis, MRI). Lack of knowledge on quantification tools reduces the amount of information that can be obtained or leads to biased quantification. The aim of this course is to provide the theoretical background on Image Analysis and to provide the student the opportunity to practice under supervision with the Program Fiji-ImageJ, one of the most used in Biomedical Research. The students will also have the opportunity to get some knowledge about the program IMARIS.

Target audience and places available. The course is mainly addressed to Master and PhD students from Biomedical Sciences-related Programs at the Universidad Autónoma de Madrid or other Universities. The 35 places will be preferentially given to the UAM students of the Master in Pharmacological Research and PhD Students from the PhD Program of Pharmacology and Physiology.

Lecturers

Dr. Ignacio Monedero Cobeta. Department of Physiology. Faculty of Medicine. Universidad Autónoma de Madrid. Email: ignacio.monedero@uam.es

Dr. Jose Mª González Granado. Department of Physiology. Faculty of Medicine. Universidad Autónoma de Madrid & Instituto de Investigación Sanitaria Hospital 12 de Octubre (Madrid). Email: josemaria.gonzalez@uam.es

Dr. Michael Schnoor. Department of Molecular Biomedicine, CINVESTAV, Mexico. Email mschnoor@cinvestav.mx.

Course design

Dr. Silvia M. Arribas Rodríguez & Dr. Ignacio Monedero Cobeta. Department of Physiology. Faculty of Medicine. Universidad Autónoma de Madrid. e-mails: silvia.arribas@uam.es, ignacio.monedero@uam.es

Course Organization

Dr. David Ramiro-Cortijo. Department of Physiology. Faculty of Medicine. Universidad Autónoma de Madrid.
e-mail: david.ramiro@uam.es

Registration and certificates

Fill the form and send it via e-mail to david.ramiro@uam.es before February, 15th. An email confirming the availability will be sent to the applicant before the course.

The seminar will be acknowledged as training activity of PhD Programs and will be awarded 2 ECTS.

To obtain a certificate the student will have to attend 80% of the sessions and to have a positive evaluation of a report of an image analysis case.

Program

Session Nº 1: Image analysis introduction

  • Image acquisition, types and properties
  • Digital image and computer analysis
  • Fiji-ImageJ software introduction
  • Imaris software introduction
  • Histogram: utilities and modification
  • Stacks and Hyperstacks
  • Practice: Applied examples of the session concepts using imageJ/ Imaris

Session Nº 2: Image Processing

  • Smoothen and noise filtering
  • Sharpening
  • Image operations
  • Fourier processing
  • Binary Image
  • Segmentation
  • ROI: region of interest
  • Practice: Applied examples of the session concepts using imageJ/ Imaris

Session Nº 3: Morphometric and Densitometric analysis

  • Morphometric object selection
  • Count and outline objects
  • Morphometry parameters
  • Densitometry parameters
  • Object analysis
  • ImageJ plugins and macro language introduction
  • Practice: Applied examples of the session concepts using imageJ/ Imaris

Session Nº 4: Specific tools and automatization design (MACROS)

  • 3D reconstruction and visualization
  • Imaris tools for 3D quantification
  • Applications of image/video acquisition and analysis.
  • Practice: Applied examples of the session concepts using imageJ/ Imaris.

Session Nº 5: Biomedical research project practical session

Application and troubleshooting of the course concepts to research projects proposed by the students.

 

Facultad de Medicina de la Universidad Autónoma de Madrid. Calle del Arzobispo Morcillo 4. 28029 Madrid. Tel. +34 91 497 54 86  Fax. 91 497 53 53. Email. informacion.medicina@uam.es