Course program overview
Course program overview
Course program overview
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PROGRAMME<br />
<strong>Course</strong> <strong>program</strong> <strong>overview</strong><br />
Note: All lectures are taking place in the ATC Flex Lab A&B.<br />
Day 1 - Monday, 15 October 2012<br />
09:00 - 10:00 Lecture by Jan Ellenberg “High throughput microscopy: From RNAi<br />
screening to in vivo proteomics”<br />
10:00 – 11:00 Lecture by Wolfgang Huber “Quality control and statistical analysis”<br />
11:00 - 11:40<br />
11:40 – 12:00<br />
Tutorial1: Beate Neumann “siRNA libraries”<br />
Tutorial 2: Sajoscha Sauer “Introduction LIMS”<br />
12:00 - 13:00 Lunch (EMBL Canteen)<br />
13:00 - 19:00 Practical workshops (P1-P4) – see outline below<br />
19:00 – 20:00 Dinner (EMBL Canteen)<br />
20:00- 22:00 Poster session with wine and cheese (Top of Helix A and ATC Lounge)<br />
22:00 Bus transfer ISG Hotel<br />
Day 2 - Tuesday, 16 October 2012<br />
09:00 - 10:00 Lecture by Jez Simpson “High content analysis strategies to dissect<br />
early secretory pathway function”<br />
10:00 - 11:00 Lecture by Paul French - “Fluorescence lifetime imaging for High Content<br />
Analysis”<br />
11:00 - 12:00 Lecture by Olli Kallioniemi – “High-throughput approaches for individualized<br />
systems medicine”<br />
12:00 - 13:00 Lunch (EMBL Canteen)<br />
13:00 - 19:00 Practical workshops (P1-P4) – see outline below<br />
19:00 – 20:00 Dinner (EMBL Canteen)<br />
20:00 - 22:00 Tutorial 2 : Kota Miura “Image J 1, J 2”<br />
22:10 Bus transfer ISG Hotel<br />
Day 3 - Wednesday, 17 October 2012<br />
09:00 - 12:00 Demonstration of HTM equipment by companies:<br />
Olympus Room ALMF / 508B<br />
"HT Acquisition and Analysis with Olympus Scan^R"<br />
GE HealthCare Room ATC / 116B<br />
PerkinElmer Room ATC / 117A<br />
“Operetta and Harmony – High Throughput Biology for Everyone”<br />
Molecular Devices Room ATC / 116A<br />
“The new ImageXpress® Micro XL from Molecular Devices - Your complete Live-Cell<br />
Imaging Solution for High Content RNAi Screens”<br />
12:00 - 13:00 Lunch (EMBL Canteen)<br />
13:00 - 19:00 Practical workshops (P5-P8) – see outline below<br />
19:00 – 20:00 Dinner (EMBL Canteen)<br />
20:00 - 21:00 Lecture by Zvi Kam – “Quantitative Microscope Image Understanding.<br />
Low and High throughput analysis”<br />
2
21:10 Bus transfer ISG Hotel<br />
Day 4 - Thursday, 18 October 2012<br />
09:00 - 10:00 Lecture by Daniel Gehrlich “Supervised and unsupervised machine<br />
learning for image-based screening”<br />
10:00-11:00 Lecture by Seamus Holden “Towards high-throughput super-resolution<br />
microscopy in bacteria”<br />
11:00 - 12:00 Lecture by Thomas Walter -"From images to gene clusters: computational<br />
approaches for phenotypic profiling"<br />
12:00 - 13:00 Lunch (EMBL Canteen)<br />
13:00 - 19:00 Practical workshops (P5-P8) – see outline below<br />
19:00 – 20:00 Dinner (EMBL Canteen)<br />
20:00 Bus transfer to ISG or downtown Heidelberg<br />
Day 5 - Friday, 19 October 2012<br />
09:00 - 10:00 Lecture by Claudia Lukas “Exploring the mammalian DNA damage<br />
response using high content siRNA screens: three short stories based<br />
on one lucky readout”<br />
10:00 -11:00 Lecture by Michael Boutros "Mapping of genetic interaction networks<br />
by RNAi and high-throughput imaging"<br />
11:00 - 12:00 Lecture by Malte Wachsmuth "High throughput FCS: parallelization<br />
and automation"<br />
12:00 - 13:00 Lunch (EMBL Canteen)<br />
13:00 - 19:00 Practical workshops (P9-P12) – see outline below<br />
19.00 - 20.00 Bus transfer via ISG to downtown Heidelberg<br />
20:00 Dinner downtown Heidelberg (Restaurant Zum Nepomuk)<br />
Individual transport to ISG Hotel<br />
Day 6 - Saturday, 20 October 2012<br />
09:00 - 10:00 Lecture by Rainer Pepperkok “High throughput microscopy approaches<br />
to disease mechanism”<br />
10:00 - 13:00 Practical workshops (P9-P12) – see outline below<br />
13:00 - 14:00 Lunch (EMBL Canteen)<br />
14:00 - 17:00 Practical workshops (P9-P12) – see outline below<br />
17:00 -18:00 Summary of the course and discussion<br />
18:10 Bus transfer to ISG Hotel<br />
3
Monday and Tuesday P1-P4<br />
Practical work<br />
P1: Coating multiwall plates ready for reverse transfection. H. Erfle and F. Neumann<br />
P2: Sample preparation. J. Bulkescher and B. Koch<br />
P3: Assay design: C. Conrad, J. Ellenberg, R. Pepperkok and J. Simpson<br />
P4: Concepts and tools for quality control. B. Fischer, J. Barry, F. Klein, Ch. Tischer<br />
Wednesday and Thursday P5-P8<br />
P5: Time-lapse acquisition of mitotic phenotypes. F. Neumann and M. Rommeswinkel<br />
(Olympus)<br />
P6: Automated FCS- data acquisition C. Conrad and M. Wachsmuth<br />
P7: Inner nuclear membrane targeting. A. Boni and Ch. Tischer<br />
P8: Microtubuli secondary screening. J. Bulkescher, F. Sieckmann and Jan Kaluza (Leica)<br />
Friday and Saturday P9-P12<br />
P9: Image analysis of P5 (time-lapse data). Ch. Sommer and T. Walter<br />
P10: Image and FCS data analysis of P6. C. Conrad and M. Wachsmuth<br />
P11: Image analysis of P7. A. Boni and K. Miura<br />
P12: Large scale analysis and Bioinformatics. B. Fischer, W. Huber, J. Barry and F.Klein<br />
Outline of the practical work<br />
Monday and Tuesday<br />
P1 Coating 96 well plates ready for transfection<br />
(ALMF screening lab / building 13, room 507)<br />
Staff: Beate Neumann, Holger Erfle<br />
Work:<br />
1. Preparation of transfection solutions with the Liquidator.<br />
2. Coating of 96 well plate<br />
3. Discussion on plate layout, QC, long-term storage.<br />
4. Inspection of coated plates.<br />
P2 Sample preparation<br />
(ALMF cell culture lab / building 13, room 505)<br />
Staff: Jutta Bulkescher, Birgit Koch<br />
Work:<br />
1. Plating cells on transfection ready 96 well plates using the cell seeding<br />
device.<br />
2. Discussion on live cell imaging requirements<br />
4
P3 Assay design<br />
(ATC / Flex Lab)<br />
Staff: C. Conrad, J. Ellenberg, R. Pepperkok and J. Simpson<br />
Blackboard Session:<br />
1. Examples of working assays, cell systems.<br />
2. Dynamic range, reproducibility, controls, specificity.<br />
3. Assay design and image analysis.<br />
4. Assays design and suitability for HCS microscopy.<br />
P4 Batch image analysis and quality control<br />
(ATC / Flex Lab B)<br />
Staff: C. Tischer<br />
Work:<br />
1. Batch image analysis using CellProfiler<br />
2. Data examination using CellProfilerAnalyst<br />
Wednesday and Thursday<br />
P5 Image acquisition time-lapse<br />
(ALMF building 13, room 508B)<br />
Staff: Beate Neumann, Matthias Rommeswinkel (Olympus)<br />
Work:<br />
1. Discussion of general set-up and functions of the microscope system.<br />
2. Optimising parameters (e.g. AF, illumination) for live cell image acquisition.<br />
3. Defining plate layout on ScanR system.<br />
4. Image acquisition by students.<br />
P6 Automated fluorescence correlation spectroscopy (FCS)<br />
(MitoSys microscopy lab / building 1D, room 4.52)<br />
Staff: Christian Conrad, Malte Wachsmuth<br />
Work:<br />
1. Introduction to manual fluorescence correlation spectroscopy (FCS)<br />
experiments<br />
2. Automated acquisition of FCS data in 96 well plates<br />
5
P7 Inner nuclear membrane targeting<br />
(ALMF / building 13, room 513)<br />
Staff: Andrea Boni, Christian Tischer<br />
Work:<br />
1. Introduction to an assay to image Inner Nuclear Membrane protein (INMP)<br />
targeting in living cells<br />
2. Setup of time-lapse microscopy experiment using confocal microscope<br />
combined with automated cell recognition and drug dispenser<br />
3. Acquisition of live cell data of INMP targeting<br />
P8 Image acquisition secondary screen<br />
(ALMF building 13, room 508F)<br />
Staff: Jutta Bulkescher, Volker Hilsenstein, Jan Kaluza, Frank Sieckmann<br />
Work:<br />
1. Automated high resolution image acquisition<br />
2. Micropilot: classifier training for automatic online classification<br />
Friday and Saturday<br />
P9 Image analysis of P5 (time-lapse data)<br />
(ATC, Flex Lab B)<br />
Staff: Christoph Sommer, Thomas Walter<br />
Work:<br />
1. Discussion of the general strategy and practical issues.<br />
2. Step-by-step analysis of time-lapse data (from P5): segmentation, feature<br />
extraction, classification (including annotation and training of a classifier)<br />
and error correction.<br />
3. Application of the workflow to selected wells and performance evaluation.<br />
4. Browsing of analysis results (prepared) and biological interpretation.<br />
P10 Image and FCS data analysis of P6 (Automated FCS)<br />
(ATC, Flex Lab A)<br />
Staff: Christian Conrad, Malte Wachsmuth<br />
Work:<br />
1. Introduction to the biophysical background of FCS and to fundamentals of<br />
data fitting<br />
2. Analysis of the data acquired during P6 (Automated FCS)<br />
6
P11 Imaging analysis of Practical 7<br />
(Cell Biology and Biophysics Unit, room 417)<br />
Staff: Kota Miura, Andrea Boni<br />
Work:<br />
1. Basic introduction to the image analysis software ImageJ<br />
2. Imaging analysis of INM targeting time lapse microscopy data using<br />
ImageJ<br />
3. Automation of imaging processing by Macro scripting<br />
P12 Large Scale Analysis and Modelling<br />
(Room 6.51A Friday / 518 A+B Saturday)<br />
Staff: Joseph Barry, Felix Klein, Bernd Fischer<br />
Work:<br />
1. Quality control of high-throughput screening data using the<br />
R/bioconductor-package cell HTS2<br />
2. Plate normalization methods, correction of spatial plate effects,<br />
and scoring<br />
3. Downstream bioinformatics analysis (gene set enrichment<br />
analysis) and interpretation<br />
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