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Automatic distance analysis in 3D-FISH experiment images.

Administrative Information


Integrative Imaging Laboratory, Institut Curie-INSERM U759.

Presentation Information

Full / Half Time Slot: Half Time Slot (25 min)

Contact / Speaker Name


Presentation Title

Automatic distance analysis in 3D-FISH experiment images.

Participant Requirements

No pre-requisite, but more suitable for cell biologists.

Biography of Speaker

Thomas Boudier received a Master in Mathematics in 1992 at University Denis Diderot, Paris, France. He received a PhD in Computer Sciences applied to Biology in 1997 at University Pierre et Marie Curie, Paris, France. He then became lecturer in 1999. He is working at the “Integrative Imaging” lab in Institut Curie, Orsay, France. He is part of European NoE “3DEM” and he is interested in 3D image processing in Biology, especially in electron tomography and confocal microscopy. He has participated in the development of numerous plugins for ImageJ such as TomoJ for electron tomography, Smart-Fish3D for analysis of F.I.S.H. images, or segmentation by active contours (snakes).


3D-Fish is a technique that permits to visualise the 3D positions of specific genes in cell nuclei. However the manual analysis of such images is complex, it requires the 3D localisation of small spots in noisy images. Furthermore in order to obtain valid statistical results, thousands of images must be analysed. We developed a plugin called Smart-3D Fish in order to automate the detection of spots (corresponding to genes labelled with FISH probes) and to calculate distances between genes. The segmentation of spots is based on biological parameters and image parameters [1]. Smart-3D Fish can handle any number of fluorescent spots and channels, it can also incorporate the images of DAPI counter-stained nuclei which can be used, for example, to normalize all measured distances according to the nuclear volume. It allowed us to analyse the relative position of genes involved in leukaemia cells[2]. The plugin was extended to allow the analysis of multi-labelled genes through a colocalization procedure, enabling the simultaneous analysis of 7 genes in cell nuclei from 3 fluorescent dyes. Last it allows the 3D registration of segmented spots positions between images allowing an extended genomic analysis. The plugin is available at
[1] Gué et al., Cytometry A. Sep;67(1):18-26.
[2] Gué et al., BMC Cancer 6:20.

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