Biology Online Module Handbook

BL4225 Advanced Microscopy and Image Analysis Seeing is Believing

(BL4225 online module handbook version 30)

cover image

image: Fluorescently labeled hemocytes (macrophage-like cells, left) and histoblasts (precursors of the adult abdominal epithelium, right) during Drosophila metamorphosis.

This module will introduce you to advanced imaging techniques, such as Confocal, Super-resolution, TIRF and Electron Microscopy and how these techniques have been utilised to address fundamental questions in Cell and Developmental Biology. You will get the opportunity to research techniques that are at the forefront of modern Biology and to develop skills in ImageJ analysis of imaging data, a skill that will be central to the advancement of bioscience in the coming years. Activities will be supplemented with research talks from academics at the cutting edge of their field and the opportunity to see advanced imaging techniques in practice.*

Credits: 15*

Semester: 1

Module Organiser
Dr Marcus Bischoff
mb273@st-andrews.ac.uk
01334 467199
Pre-requisite Modules:
Before taking this module you must pass BL3303 or pass BL3315*
Anti-requisite Modules:
You cannot take this module if you take BL5420*
Post-requisite Modules:
*
Additional Module Information:
Please check MMS regularly for additional module information


Biology Teaching Office:
The Biology Hive, New Technology Centre, University of St Andrews, North Haugh, St Andrews, Fife KY16 9SR

Email: bioteach@st-andrews.ac.uk      Tel: 01334  463602

BL4225: Timetable

Legend (not all modules have every event type):
lecture
tutorial
workshop
practical
other

Semester 1: Week 1

DATE & TIMEVENUESTAFFEVENT
Monday
17-09-2018
09:00 to 11:00
Medical and Biological Sciences Building
Tutorial Room 13
Dr Marcus Bischoff

Lecture L1: Basics of light microscopy
2018-9_BL4225_L1
Tuesday
18-09-2018
11:00 to 13:00
Purdie Building
Purdie Seminar Room 222
Dr Marcus Bischoff

Lecture L2: Fluorescence microscopy
2018-9_BL4225_L2

Semester 1: Week 2

DATE & TIMEVENUESTAFFEVENT
Tuesday
25-09-2018
11:00 to 13:00
Purdie Building
Purdie Seminar Room 222
Dr Marcus Bischoff
Dr Carlos Penedo-Esteiro
Dr Jens Tilsner
Lecture L3: Super-resolution microscopy + TIRF microscopy and single molecule imaging
2018-9_BL4225_L3

Semester 1: Week 3

DATE & TIMEVENUESTAFFEVENT
Tuesday
02-10-2018
11:00 to 13:00
Purdie Building
Purdie Seminar Room 222
Dr Marcus Bischoff

Workshop W1: ImageJ Workshop 1
2018-9_BL4225_W1

Semester 1: Week 4

DATE & TIMEVENUESTAFFEVENT
Tuesday
09-10-2018
11:00 to 13:00
Purdie Building
Purdie Seminar Room 222
Dr Marcus Bischoff

Lecture L4: ImageJ Workshop 2
2018-9_BL4225_L4

Semester 1: Week 5

DATE & TIMEVENUESTAFFEVENT
Tuesday
16-10-2018
11:00 to 13:00
Purdie Building
Purdie Seminar Room 222
Dr Marcus Bischoff
Dr Stefan Pulver
Dr Judith Sleeman
Lecture L5: Fluorescence techniques to study protein function + Measuring and manipulating neural activity with light
2018-9_BL4225_L5

Semester 1: Week 7

DATE & TIMEVENUESTAFFEVENT
Tuesday
30-10-2018
11:00 to 13:00
Purdie Building
Purdie Seminar Room 222
Dr Marcus Bischoff
Dr John Lucocq
Lecture L6: Electron microscopy + ImageJ Workshop 3
2018-9_BL4225_L6

Semester 1: Week 8

DATE & TIMEVENUESTAFFEVENT
Tuesday
06-11-2018
11:00 to 13:00
Purdie Building
Purdie Seminar Room 222
Dr Marcus Bischoff
Dr Carlos Penedo-Esteiro
Tutorial T1: Student presentations
2018-9_BL4225_T1
Wednesday
07-11-2018
09:00 to 11:00
Medical and Biological Sciences Building
Seminar Room 2
Dr Marcus Bischoff
Dr Carlos Penedo-Esteiro
Tutorial T2: Student presentations
2018-9_BL4225_T2

Semester 1: Week 9

DATE & TIMEVENUESTAFFEVENT
Tuesday
13-11-2018
11:00 to 13:00
Purdie Building
Purdie Seminar Room 222
Dr Marcus Bischoff
Dr Carlos Penedo-Esteiro
Tutorial T3: Student presentations
2018-9_BL4225_T3

Semester 1: Week 11

DATE & TIMEVENUESTAFFEVENT
Tuesday
27-11-2018
11:00 to 13:00
Biomolecular Sciences Building
tba
Dr Marcus Bischoff
Dr John Lucocq
Dr Carlos Penedo-Esteiro
Workshop W2: Demonstration of advanced imaging systems
2018-9_BL4225_W2
Data Sources: information in this online module handbook is gathered from several sources.
Small footnote marks beside content, or by section titles indicate the source.
* University of St Andrews Module Catalogue
School of Biology Symbiosis Database (module organisers only)
University of St Andrews MMS (St Andrews users only)

BL4225: Assessment

1.5-hour Written Examination = 20%, Coursework = 80%*

Assessment:
Presentation
Due by:
16/11/2018 17:00
Feedback due by:
07/12/2018 17:00
Type:
Turnitin
Weight:
37.5%
Assessment:
Figure and Legend
Due by:
23/11/2018 17:00
Feedback due by:
14/12/2018 17:00
Type:
Turnitin
Weight:
62.5%

(MMS assessment data cached: 14 November 2018 23:20:08.)


The following related information applies to all Biology modules:

School of Biology Marking Criteria: See School of Biology Undergraduate Handbook
Late submission of continuous assessment work:

All late submissions of coursework that do not require electronic submission should be made via the late submissions box in the Biomolecular Science Building (beside the Teaching Office)
Exam details: See School of Biology Undergraduate Handbook
Exam timetable: see http://www.st-andrews.ac.uk/students/academic/examinations/examtimetablescurrent/
Expected attendance: See School of Biology Undergraduate Handbook for detailed attendance requirements.
Good Academic Practice & Avoiding Academic Misconduct: See School of Biology Undergraduate Handbook
University Student Handbook: University Student Handbook
School and University regulations in the School and University Undergraduate Handbook relating to absence reporting, penalties and rules for late submission of work, extensions for coursework, return of coursework, S-coding, good academic practice and Academic Alerts.: School of Biology Undergraduate Handbook University Student Handbook
Data Sources: information in this online module handbook is gathered from several sources.
Small footnote marks beside content, or by section titles indicate the source.
* University of St Andrews Module Catalogue
School of Biology Symbiosis Database (module organisers only)
University of St Andrews MMS (St Andrews users only)

Who to ask

(Information in this section applies to all Biology Modules)

Questions about different aspects of the module should be directed to different people:

Questions about Contact
General teaching matters Biology Teaching Office ( bioteach@st-andrews.ac.uk )
Rescheduled or cancelled events Check your University email
Lecture or practical content The lecturer who presented the material
Completing assessed practical assignments The lecturer who set the assignment
Completing assessments Module Organiser (Dr Marcus Bischoff mb273@st-andrews.ac.uk)
Marking on continuous assessment The Demonstrator or Module Organiser (Dr Marcus Bischoff mb273@st-andrews.ac.uk)
Marking on exams Module Organiser (Dr Marcus Bischoff mb273@st-andrews.ac.uk)
Rearranging practical days Grant Brown
Absence and/or extensions Module Organiser (Dr Marcus Bischoff mb273@st-andrews.ac.uk) and the Biology Teaching Office ( bioteach@st-andrews.ac.uk )

Difficulties with academic progress which impact more than one module:

Year Coordinator

See School of Biology Undergraduate student handbook for list: http://biology.st-andrews.ac.uk/documents/UndergraduateHandbook.pdf

Overall performance, progress or future directions:

Advisor of Studies

Disability:

Disability Coordinator (Dr Jacqueline Nairn jn37@st-andrews.ac.uk)

Biology Teaching Office:

The Biology Hive, New Technology Centre, University of St Andrews, North Haugh, St Andrews, Fife KY16 9SR

Email: bioteach@st-andrews.ac.uk

Tel: 01334 463602

BL4225: Contributing Staff

Dr Marcus Bischoff

Dr Marcus Bischoff
(Module Organiser)

Lecturermb273@st-andrews.ac.uk
Dr Marcus BischoffDr Marcus Bischoff
(Module Organiser)
Lecturermb273@st-andrews.ac.uk
Dr John LucocqDr John LucocqReaderjml7@st-andrews.ac.uk
Dr Carlos Penedo-EsteiroLecturerjcp10@st-andrews.ac.uk
Dr Stefan PulverDr Stefan PulverLecturersp96@st-andrews.ac.uk
Dr Judith SleemanDr Judith SleemanSenior Lecturer in Cell and Developmental Biologyjes14@st-andrews.ac.uk
Dr Jens TilsnerDr Jens TilsnerLecturerjt58@st-andrews.ac.uk
Data Sources: information in this online module handbook is gathered from several sources.
Small footnote marks beside content, or by section titles indicate the source.
* University of St Andrews Module Catalogue
School of Biology Symbiosis Database (module organisers only)
University of St Andrews MMS (St Andrews users only)

BL4225: Learning Outcomes

Students completing module BL4225 successfully should be able to:

  • Acquire an understanding of different imaging techniques
  • Understand their applications in Cell and Developmental Biology
  • Be familiar with image processing and analysis techniques
  • Find and critically evaluate information/literature
  • Produce a concise figure legend
  • Give a presentation, group discussion
  • Use Excel and ImageJ, basic statistical analysis
  • Produce a scientific figure
Data Sources: information in this online module handbook is gathered from several sources.
Small footnote marks beside content, or by section titles indicate the source.
* University of St Andrews Module Catalogue
School of Biology Symbiosis Database (module organisers only)
University of St Andrews MMS (St Andrews users only)

BL4225: Acquired Skills

Practical Skills

  • Image analysis
  • Image processing

Transferable Skills

  • Long individual presentation on given topic (>15 min)
  • Critically evaluating sources/information
  • Finding literature
  • Sourcing figures/tables
  • Data analysis
  • Descriptive statistics
  • Produce graphs/figures
  • Use other data analysis software
Data Sources: information in this online module handbook is gathered from several sources.
Small footnote marks beside content, or by section titles indicate the source.
* University of St Andrews Module Catalogue
School of Biology Symbiosis Database (module organisers only)
University of St Andrews MMS (St Andrews users only)

Policies

(Information in this section applies to all Biology Modules)