====== FIJI Hackathon 2010 ======
===== On Arrival =====

On arrival to EMBL Heidelberg, please go to the reception at the main entrance, and register as a EMBL guest. You will receive a Guest ID card. Please also ask the reception to call Kota Miura (**ex 8404**).

 If you could not find me, then please go to the room 6.51a directly. 

===== Welcome event =====

Starts from 14:00, on March 15, 2010 (Mon) @ Room6.51a, EMBL Heidelberg. 
Aim is to introduce oneself to each other.  Other schedule for the hackathon is still open. 
===== commuting between ISG Hotel and EMBL =====

  - At 8:40AM, a special shuttle bus for the Hackathon members will pick you up at the ISG hotel and bring you up to EMBL. 

  - Takes 20 - 30 minutes on foot. 

Shuttle bus is available during morning and evening. \\
http://www.embl.de/aboutus/contact/shuttle/embl_shuttle.pdf

For going downtown, please visit\\
http://www.embl.de/aboutus/contact/shuttle/index.html

===== Others =====

  * lunch will be  at the canteen, 12:00 Mon-Fri.
  * in the room you should find coffee, tee and some small treats.
  * dinner is at 7pm in the small canteen (also called old canteen).
  * for LAN connection, please ask Kota. Be prepared with MAC addresses of both LAN and WLAN adapters.
====== FIJI/ImageJ Tutorials/Workshops ======
Fiji/ImageJ hands-on tutorials by FIJI Hackers
===== day 1 =====

7/3 (Wed, 2:30pm-5:00pm in Room 202)\\
**Image segmentation workshop**

This hands-on tutorial will demonstrate how to use Fiji plugins for
image segmentation in biological images.
Examples included:
  * 3D confocal stacks
  * 2D particle counting
  * electron microscopy segmentation
The algorithms will be: SIOUX, Level Sets, and a trainable machine
learning plugin.

Instructors:\\
Arganda/Frise/Longair/Schindelin

  - SIOX: Simple Interactive Object Extraction ([[http://pacific.mpi-cbg.de/wiki/index.php/SIOX:_Simple_Interactive_Object_Extraction |Link]])
    - Instructor: Ignacio Arganda_Carreras
    - example used: "embryo"
  - Level-set [[http://pacific.mpi-cbg.de/wiki/index.php/Level_Sets | Link]]
    - Instructor: Erwin Frise
    - example used: "dot-brot", "mri-stack"
  - NeuriteTracer [[http://pacific.mpi-cbg.de/~longair/examples/ |Link]]
    - Instructor: Mark Longair
    - example used: "example_for_tracing"
===== day 2 =====

18/3 (Thu, 2:30pm-5:00pm in Room 202):\\
**Image registration workshop**

We'll demonstrate how to stitch large montages of images using
phase-correlation (fast) and feature extraction (very precise).
For both linear and non-linear (warping).

Instructors:\\
Saalfeld/Preibisch/Arganda/Cardona

  - EM image stitching using TrakEM2
    - Instructor: Stephane Saarfeld
  - EM image registration in Z-axis bUnwarpJ
    - Instructor: Ignacio  

===== Instructions before the tutorial =====

please bring a laptop with you, and before you are arriving, please install FIJI.

Installation is not difficult. Just download and unpack. Instructions are in  below.

http://pacific.mpi-cbg.de/wiki/index.php/Downloads

If you are using Windows and not sure if your laptop is 32-bit or 64-bit, please write to me.

For MacOSX  1.5 or below, you need to [[http://pacific.mpi-cbg.de/wiki/index.php/MacOSX_tips#Running_Fiji_on_Java_1.5_.2832-bit.29 | follow another step]].


** maybe you could bring your own image data and ask instructors to demonstrate segmentation or registering the image using FIJI.**

====== Talks ======

===== Erwin Frise 17/3 (Wed) =====

  * 11am @Small Operon
**“Exploring spatial gene expression during early development of Drosophila”**

<blockquote>
Exploring spatial gene expression during early development of Drosophila

Erwin Frise, Ann S. Hammonds, Susan E. Celniker
Berkeley Drosophila Genome Project, Lawrence Berkeley Natl. Labs, Berkeley, CA 94720

To analyze regulatory networks in multicellular organisms, it is essential to know both spatial and temporal patterns of genes expression. We are generating a 2D mRNA expression atlas to profile embryonic development of Drosophila. To utilize the image dataset for computational analysis, we converted images into standardized virtual representations of expression patterns that we called Triangulated Images (TIs). TIs provide an intuitive representation in which spatial expression can be visualized in context of other genes and analyzed using standard computational tools. We have demonstrated the utility of our approach in a systematic analysis of the gene expression dataset and have made the TIs available to the community
.
We have now extended the dataset to over 7,500 genes and completed collecting images of expression patterns for over 97% of the set of 711 sequence specific Transcription Factors (TF) identified by manual curation of genes with known or predicted DNA binding domains. The inclusion of nearly all TF expression patterns greatly enhances the use of our dataset for identifying components of regulatory networks. We will present novel interactive visualization tools and strategies to organize and refine experimentally and computationally derived datasets.

</blockquote>
===== Pavel Tomancak 19/3 (Fri) =====

  * 11am @Small Operon
**“New tricks for comparative genomics analysis of gene expression regulation in Drosophila”**

===== Mark Longair 24/3 (Wed) =====

  * 4pm @Small Operon
**“Neuron Tracing and Computational Neuroanatomy with Free Software”**

====== contacts ======

Elisabeth Hillier (DB Secretary ex 8165)\\
Kota Miura (ex 8404)\\
Francesca Peri (ex 8414)\\