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EMBL BioImage Data Analysis



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RT @EPFL_Imaging: ⏰ Introduction Workshop on ImageJ/Fiji for EPFL Students and Postdocs. Imaging Lunch #3 on December 14, 2022 at 11: 00, R…
About 2 days, 8 hours ago by: Kota Miura (@cmci_)

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RT @Dr_Lori_Burrows: Robust fluorescent proteins for high-resolution microscopy and biochemical techniques | Nature Methods
About 3 days, 2 hours ago by: Kota Miura (@cmci_)

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This is a huge contribution to the community!
About 3 days, 2 hours ago by: Kota Miura (@cmci_)

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RT @BioDecoded: AutoDeconJ: a GPU accelerated ImageJ plugin for 3D light field deconvolution with optimal iteration numbers predicting | Bi…
About 3 days, 3 hours ago by: Kota Miura (@cmci_)

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RT @ArrateMunoz: Are you developing image processing pipelines and not knowing the best way to make your code easily accessible and reprodu…
About 3 days, 3 hours ago by: Kota Miura (@cmci_)

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RT @ColauttiLab: First public release of R Crash Course for Biologists. Link to (free) PDF or EPUB and (paid) Kindle, hard cover (colour) o…
About 3 days, 3 hours ago by: Kota Miura (@cmci_)

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

  1. 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.
  1. Takes 20 - 30 minutes on foot.

Shuttle bus is available during morning and evening.

For going downtown, please visit


  • 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.


  1. SIOX: Simple Interactive Object Extraction (Link)
    1. Instructor: Ignacio Arganda_Carreras
    2. example used: “embryo”
  2. Level-set Link
    1. Instructor: Erwin Frise
    2. example used: “dot-brot”, “mri-stack”
  3. NeuriteTracer Link
    1. Instructor: Mark Longair
    2. 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).


  1. EM image stitching using TrakEM2
    1. Instructor: Stephane Saarfeld
  2. EM image registration in Z-axis bUnwarpJ
    1. 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.

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 follow another step.

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


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”


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

meeting/fiji2010.txt · Last modified: 2020/11/26 09:11 (external edit)