4th Training School, Vodnany (Czech Republic), March 2015

Optical Microscopy and Image Analysis
Vodnany (Czech Republic), 16th – 20th March 2015

Scientific report

The 4th Training School of the AQUAGAMETE COST Action, entitled “ Optical Microscopy and Image Analysis”, was held at the University of Ceske-Budejovice, in the Faculty of Fisheries and Quality of Water, in Vodnany, Czech Republic, from 16th – 20th March 2015.

The course was organized by Dr. Jacky Cosson and Dr. Martin Psenicka with the assistance of part of the staff of this Faculty. There were 19 students from 10 different countries attending the TS, most of them preparing a PhD. Nine expert trainers and lecturers presented lectures and participated to practical classes.
The Training School consisted each day in morning lectures and practical sessions in the afternoon using regular, fluorescence and confocal microscopes, as well as training exercises of image analysis using several softwares (Image J, Mathlab and CASA).
A group of lectures constituting the major core of the formal presentations were by C. Matthews and C. Rouvière, mostly dealing on “The principles of Optical Microscopy and of Image Analysis“. In addition, one lecture was presented by Prof. D. Stys on the “Principles of image build-up in the microscope“. A second lecture was presented by Dr G. Prulières on “Application of fluorescence and confocal microscopy to aquatic eggs“. A third lecture was by Dr H. Gadêlha on the “Modelisation and quantitative predictions of cell behavior, especially spermatozoa“. A fourth lecture was by Dr R. Rychtarikova on the “Analysis of cell interior – 3D reconstruction“. A fifth lecture was by Prof. C. Soler Vázquez, entitled “Presentation of CASA (sperm motility parameters) and cell morphometry soft-wares“. Two extra lectures were presented, one by – T. Nahlik on “The use of software dedicated to follow-up of microscope images” and another by J. Nebesarova on “Cryo-Electron Microscope Tomography“.
The practice groups (4 people/ each group) were organized by rotation between the following practices: Practice 1 was dealing with “Setting up the microscope, alignment, observations using different optical techniques“, Practice 2: “Confocal microscopy“, Practice 3: “Sperm motility (CASA)“, Practice 4: “Fixation and immuno-staining on fixed oocytes“, Practice 5: “Immuno-staining and mounting of eggs“, Practice 6: “Quantitative cell behavior modelisation“. Informal meeting groups were organized between many of the trainers and trainees: those working groups involved practices of ImageJ software and its Plug-ins, as well as Mathlab practices.
On the first day, before the lectures, the trainees made short presentations to introduce themselves, and talk about their current research, interests or concerns on the different topics of the course.
On the last day, after the last session, the trainees were invited to formulate their appreciation on the general level of the teaching that they received and some proposed minor possible improvements for future. The quality of the training school was evaluated as excellent/very good, considering the balance between their expectations and the accomplished objectives. Altogether, the TS allowed development of a networking between trainees and trainers leading to pursue the work initiated during the TS period.

NEW!! The presentations given by the trainers during this course can be downloaded by clicking in the following link: https://dl.dropboxusercontent.com/u/4171860/PPTs%3CTRainers.zip

Family picture

Second announcement and programme

DATES: 16th to 20th March 2015
PLACE: Faculty of Fisheries and Protection of Waters USB, Vodnany, Czech Republic

Deadline for applications extended to January 20th.

MAIN TRAINERS FOR PRACTICE:
• H. Gadêlha: Wolfson Centre for Mathematical Biology, Mathematical Institute, University of Oxford
• C. Matthews, IBDML, CNRS, Marseille, France.
• C. Rouvière, Biologie du développement, CNRS, Villefranche sur mer, France.
• G. Prulières: Biologie du développement, CNRS, Villefranche sur mer, France.
LECTURERS:
• J. Cosson and G. Prokopchuk, FFPW USB, Vodnany, Czech Republic
 Sperm motility recording; use of high-speed video camera
• C. Soler Vázquez, PROISER R+D S.L., Valencia, Spain
 Presentation of some soft-wares = CASA (sperm motility parameters) and cell morphometry
• G. Prulières, Biologie du développement, CNRS, Villefranche sur mer, France
 Application of fluorescence and confocal microscopy to aquatic eggs
• R. Rychtarikova, FFPW USB, ICS, Nove Hrady, Czech Republic
 Analysis of cell interior – 3D reconstruction
• D. Stys, FFPW USB, ICS, Nove Hrady, Czech Republic
 Principles of image build-up in the microscope
• T. Nahlik, FFPW USB, ICS, Nove Hrady, Czech Republic
 Training on the use of software dedicated to follow-up of microscope images
• H. Gadêlha, Dept of Applied Mathematics and Theoretical Physics, Cambridge, UK
 Modelisation and quantitative predictions of cell behavior
• B. Dzyuba, FFPW USB, Vodnany, Czech Republic
 Applications of CASA analysis to fish spermatozoa
TRAINEES: 12 maximum

PROGRAM MONDAY 16. 3. 2015
9:30 – 10:00 Registration (local fees)
10:00 – 10:30 Welcome introduction: Presentation of participants / round table
10:30 – 10:45 Coffee break
10:45 – 12:30 Presentation by D. Stys: Principles of image build-up in the microscope
12:30 – 13:30 Lunch break
13:30 – 15:30 Presentation by C. Soler Vázquez: Presentation of some soft-wares = CASA (sperm motility parameters) and cell morphometry
15:30 – 15:50 Coffee break
15:50 – 17:50 Presentations by C. Matthews and C. Rouvière: Fluorescence & overview of Fluorophores

PROGRAM TUESDAY 17. 3. 2015
9:00 – 10:30 Presentations by C. Matthews and C. Rouvière: Microscopy technics (Bright field / dark field / DIC / Phase / polarization / fluorescence)
10:30 – 10:45 Coffee break
10:45 – 12:30 Presentations by C. Matthews and C. Rouvière: Confocal microscopy
12:30 – 13:30 Lunch break
13:30 – 15:30 Practice 1 Group A; Practice 2 Group B; Practice 4 Groups C+D
15:30 – 15:50 Coffee break
15:50 – 17:50 Practice 1 Group C; Practice 2 Group D; Practice 4 Groups A+B

WEDNESDAY 18. 3. 2015
9:00 – 10:30 Presentations by C. Matthews and C. Rouvière: Optical sectioning microscopies
10:30 – 10:45 Coffee break
10:45 – 12:30 Presentations by C. Matthews and C. Rouvière: Image treatment and analysis
12:30 – 13:30 Lunch break
13:30 – 15:30 Practice 1 Group B; Practice 2 Group A; Practice 5 Groups C+D
15:30 – 15:50 Coffee break
15:50 – 17:50 Practice 1 Group D; Practice 2 Group C; Practice 5 Groups A+B
18:00 – 19:00 Practice 6 Groups A+B

THURSDAY 19. 3. 2015
9:00 – 10:30 Presentation by G. Prulière: Application of fluorescence and confocal microscopy to aquatic eggs
10:30 – 10:45 Coffee break
10:45 – 12:30 Practice 1, ImageJ software
12:30 – 13:30 Lunch break
13:30 – 15:30 Practice 2, “ImageJ” software
15:30 – 15:50 Coffee break
15:50 – 17:30 Practice / ImageJ macro
18:00 – 19:00 Practice 6 Group C+D

FRIDAY 20. 3. 2015
9:00 – 10:30 Presentation by R. Rychtarikova: Analysis of cell interior – 3D reconstruction
10:30 – 10:45 Coffee break
10:45 – 12:30 Presentation by H. Gadêlha: Modelisation and quantitative predictions of cell behavior
12:30 – 13:30 Lunch break
13:30 – 15:30 Presentation & training by T. Nahlik: Training on the use of software dedicated to follow-up of microscope images
15:30 – 15:50 Coffee break
15:50 – 17:00 Training by T. Nahlik (continued)

PRACTICE GROUPS:
 4 people/ each group called A, B, C, D
 Practice 1: Setting up the microscope, alignment, observations using different optical techniques
 Practice 2: Confocal microscopy
 Practice 3: Sperm motility (CASA)
 Practice 4: fixation and immuno-staining on fixed oocytes 1/2
 Practice 5: immuno-staining and mounting 2/2
 Practice 6: quantitative cell behavior modelisation

Second announcement and programme Vodnany

First Announcement

Dear colleagues,

The AQUAGAMETE COST Action (aquagamete.webs.upv.es/web) is pleased to announce the 4th AQUAGAMETE Training School. This Training School is aimed towards young researchers (PhD students, young post-docs and MSc students) as well as representatives from industry. The course will be focused on Optical Microscopy Techniques and Image Analysis Facilities assisted by Computer used in Reproductive Biology, potentially applicable to aquatic gametes and early embryos. Various aspects of expertise and topics will be covered, such as:

* Principles of optical microscopy techniques applied to Biology.
* Practical applications of optical combinations: phase-contrast, differential interference contrast, dark-field, fluorescence, confocal and optical sectioning microscopy.
* Collection of images generated by a microscope: photo- or video-cameras, including high-speed video-cameras.
* Computer assisted image analysis applied to fast moving microscopic objects like spermatozoa or to large and still objects like eggs.
* Data analysis using different soft-wares dedicated to these applications: CASA, Image J plug-ins, cell morphometry soft-wares, etc.
* Modelisation and quantitative predictions of cell behavior.

The 4th AQUAGAMETE Training School will highlight the most recent developments in each topic, thanks to invited lecturers so as to promote a strong interaction between trainees working on different aspects of Reproductive Biology of Aquatic Gametes and experienced trainers as specialists in the use, improvement and development involved in the above-mentioned Optical and Computer applications.

The Training Course will take place from 16th to 20th of March 2015 in the facilities of the Faculty of Fisheries and Quality of Waters, in Vodnany (Czech Republic) and its organization will rely mostly on the staff of the Laboratory of Reproductive Physiology belonging to the Research Institute of Fish Culture and Hydrobiology, with assistance of members of the Institute of Complex Systems.

For efficiency reasons, good level of know-how transfer and practical access of trainees to microscopes, the number of participants will be restricted to 12 trained persons. Financial support from the AQUAGAMETE COST Action will be available for students. Registration fee for students (250 euros) and for industry representatives (400 euros) will include all lunches and breakfasts, accommodation for 5 nights, access to lectures and laboratory practices, support material, transport between facilities and main accommodation place.

The application deadline is 10th of January 2015 and complete applications must be sent via e-mail to aquagamete@gmail.com. Eligible candidates will be announced by the 7th of February 2015. For more detailed information, you can e-mail your message to local contacts: Jacky Cosson (jacosson@gmail.com) or Klára Kovaříková (kkovarikova@frov.jcu.cz).

Applications should include:

* Application form;
* Short Curriculum Vitae in the area (only for students);
* Motivation letter for participating in the training school, which should indicate 
the academic/professional status of the applicant;
* Letter of recommendation from the applicant’s supervisor or employer;
* Financial Support justification (only for students), in which trainees should make an estimation of their expenses during the week of the Training School.

We would appreciate if you could forward this announcement via e-mail to colleagues or students who may be interested in participating.

Practical information: Closest city with international airport is Prague (PRAHA). We shall try to arrange a shuttle bus to lead attendants from Prague airport to our Faculty in Vodnany. Also, a shuttle bus would be organized to drive your from local accommodation place to our Institute.

More information will be available soon at: http://aquagamete.webs.upv.es/

Files to download:
First Announcement Training School Vodnany
Application form training school Vodnany 201503