Automatic analysis of light and electron microscopy neuronal data
Project goals
This project is a small part of an effort to obtain what is sometimes called the 'brain wiring diagram' - a detailed description of a part of the neural tissue, the sizes, shapes, types and positions the neurons in the tissue and especially their connectivity pattern, the geometry of the axons and dendrites, the size of the synapses and perhaps other parameters of interest. We plan to develop algorithms for the joint analysis of 3D light microscopy (mainly confocal microscopy and two-photonmicroscopy) and 3D electron microscopy (mainly a focused ion beamscanning electron microscopy, FIB/SEM), which will segment the 3Delectron microscopy images with the help of the light microscopy images, identifying and classifying the neurons and various other subcellular structures. We will also automatically trace the dendrites and axons, forming a tree and determining connectivity between the neurons. An important part of the project will be the development of technique for registering electron and light microscopy images.
Keywords
electronmicroscopy3Dimageprocessingneuronssegmentationimageregistration
Public support
Provider
Czech Science Foundation
Programme
Standard projects
Call for proposals
Standardní projekty 14 (SGA02011GA-ST)
Main participants
—
Contest type
VS - Public tender
Contract ID
P202-11-0111
Alternative language
Project name in Czech
Automatická analýza obrazů nervové tkáně ze světelné a elektronové mikroskopie
Annotation in Czech
Navrhovaný projekt ja částí širšího úsilí k získání "schématu mozku" - detailního popisu části nervové tkáně, typů a pozic neuronů v tkáni a jejich propojení, geometrie axonů a dendritů, velikosti synapsí a dalších parametrů. Vyvineme algoritmypro společnou analýzu obrazů ze světelné mikroskopie (zejména konfokální a dvoufotonové) a 3Delektronové mikroskopie (hlavně FIB/SEM - rastrovací mikroskop siontovým svazkem), které budou umět segmentovat 3D obrazy z elektronové mikroskopie za pomoci obrazů z mikroskopie světelné. Budeme identifikovat a klasifikovat neurony a další subcelulární struktury. Automaticky vytvoříme strom dendritů a axonů a určíme propojení mezi neurony. Důležitou součástí práce bude registrace obrazů z obou modalit.
Scientific branches
R&D category
ZV - Basic research
CEP classification - main branch
IN - Informatics
CEP - secondary branch
JD - Use of computers, robotics and its application
CEP - another secondary branch
EE - Microbiology, virology
10201 - Computer sciences, information science, bioinformathics (hardware development to be 2.2, social aspect to be 5.8)
10606 - Microbiology
10607 - Virology
20204 - Robotics and automatic control
20205 - Automation and control systems
Completed project evaluation
Provider evaluation
U - Uspěl podle zadání (s publikovanými či patentovanými výsledky atd.)
Project results evaluation
The project resulted in a sequence of quality and original results in the field of automated bio-medical image processing. The final project resume is adequate. Several students were involved. The project results can be applied in medicine. The project outcomes appeared in top-ranked journals in the field and were presented at good conferences. No formal issues were found.
Solution timeline
Realization period - beginning
Jan 1, 2011
Realization period - end
Dec 31, 2014
Project status
U - Finished project
Latest support payment
Apr 18, 2014
Data delivery to CEP
Confidentiality
S - Úplné a pravdivé údaje o projektu nepodléhají ochraně podle zvláštních právních předpisů
Data delivery code
CEP15-GA0-GA-U/01:1
Data delivery date
May 22, 2015
Finance
Total approved costs
4,444 thou. CZK
Public financial support
4,444 thou. CZK
Other public sources
0 thou. CZK
Non public and foreign sources
0 thou. CZK
Basic information
Recognised costs
4 444 CZK thou.
Public support
4 444 CZK thou.
100%
Provider
Czech Science Foundation
CEP
IN - Informatics
Solution period
01. 01. 2011 - 31. 12. 2014