meeting:fiji2010
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| meeting:fiji2010 [2010/03/16 15:01] – kota | meeting:fiji2010 [2020/11/26 09:11] (current) – external edit 127.0.0.1 | ||
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| ===== commuting between ISG Hotel and EMBL ===== | ===== commuting between ISG Hotel and EMBL ===== | ||
| - | Takes 20 - 30 minutes on foot. | + | - 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. \\ | Shuttle bus is available during morning and evening. \\ | ||
| Line 19: | Line 21: | ||
| For going downtown, please visit\\ | For going downtown, please visit\\ | ||
| http:// | http:// | ||
| + | |||
| ===== Others ===== | ===== Others ===== | ||
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| * dinner is at 7pm in the small canteen (also called old canteen). | * 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. | * for LAN connection, please ask Kota. Be prepared with MAC addresses of both LAN and WLAN adapters. | ||
| - | |||
| ====== FIJI/ImageJ Tutorials/ | ====== FIJI/ImageJ Tutorials/ | ||
| - | Fiji/ImageJ hands-on tutorials | + | Fiji/ImageJ hands-on tutorials |
| ===== day 1 ===== | ===== day 1 ===== | ||
| Line 36: | Line 38: | ||
| image segmentation in biological images. | image segmentation in biological images. | ||
| Examples included: | Examples included: | ||
| - | | + | |
| - | | + | |
| - | | + | |
| The algorithms will be: SIOUX, Level Sets, and a trainable machine | The algorithms will be: SIOUX, Level Sets, and a trainable machine | ||
| learning plugin. | learning plugin. | ||
| Line 45: | Line 47: | ||
| Arganda/ | Arganda/ | ||
| + | - SIOX: Simple Interactive Object Extraction ([[http:// | ||
| + | - Instructor: Ignacio Arganda_Carreras | ||
| + | - example used: " | ||
| + | - Level-set [[http:// | ||
| + | - Instructor: Erwin Frise | ||
| + | - example used: " | ||
| + | - NeuriteTracer [[http:// | ||
| + | - Instructor: Mark Longair | ||
| + | - example used: " | ||
| ===== day 2 ===== | ===== day 2 ===== | ||
| Line 56: | Line 67: | ||
| Instructors: | Instructors: | ||
| Saalfeld/ | Saalfeld/ | ||
| + | |||
| + | - EM image stitching using TrakEM2 | ||
| + | - Instructor: Stephane Saarfeld | ||
| + | - EM image registration in Z-axis bUnwarpJ | ||
| + | - Instructor: Ignacio | ||
| ===== Instructions before the tutorial ===== | ===== Instructions before the tutorial ===== | ||
| Line 67: | Line 83: | ||
| If you are using Windows and not sure if your laptop is 32-bit or 64-bit, please write to me. | If you are using Windows and not sure if your laptop is 32-bit or 64-bit, please write to me. | ||
| - | For MacOSX | + | For MacOSX |
| - | http:// | + | |
| + | |||
| + | ** 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”** | ||
| + | |||
| + | < | ||
| + | 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. | ||
| + | |||
| + | </ | ||
| + | ===== 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”** | ||
| - | ** maybe you could bring your own image data and ask instructors to demonstrate segmentation or registering the image using FIJI. | ||
| ====== contacts ====== | ====== contacts ====== | ||
meeting/fiji2010.1268751700.txt.gz · Last modified: 2016/05/24 12:46 (external edit)