CNN for calcium signal classification in astrocytes observed with 3D lattice light sheet fluorescence microscopy
Contract type : Internship agreement
Level of qualifications required : Bachelor's degree or equivalent
Fonction : Internship Research
Context
Astrocytes are glial cells in the central nervous system that recently emerged as key partners of neurons for the processing of information. Astrocytic calcium signals are involved in many key brain functions (e.g., memory and learning), and their alterations can lead to brain diseases. These signals also exhibit an important spatiotemporal diversity, and it is still unknown whether this variability relates to their role in distinct neurobiological functions. Not surprisingly, decoding this calcium code is a leading topic in neuroscience. The recent emergence of lattice light sheet microscopy (LLSM) now enables a 3D imaging with high spatiotemporal resolution of these signals. Unfortunately, the community is currently lacking of image analysis tools to detect, segment and quantify these signals in LLSM images.
Assignment
In this context, we are developing an image processing tool for neurobiologists which 1) detects and segments calcium signals in 3D+time LLSM images, and 2) classifies these signals based on their 3D space-time morphological characterization. To do so, we focus on unsupervised 3D convolutional network and machine learning techniques.
Main activities
Main goals:
- Development of an unsupervised CNN to classify different types of calcium signals
- Development of a napari plugin to annotate 3D+time data
Skills
Technical skills and level required : image processing and analysis, deep learning (CNNs), Python, and Keras, Tensorflow or Pytorch.
General Information
- Theme/Domain :
Computational Biology
Biologie et santé, Sciences de la vie et de la terre (BAP A) - Town/city : Rennes
- Inria Center : Centre Inria de l'Université de Rennes
- Starting date : 2024-03-01
- Duration of contract : 6 months
- Deadline to apply : 2024-04-30
Warning : you must enter your e-mail address in order to save your application to Inria. Applications must be submitted online on the Inria website. Processing of applications sent from other channels is not guaranteed.
Instruction to apply
Defence Security :
This position is likely to be situated in a restricted area (ZRR), as defined in Decree No. 2011-1425 relating to the protection of national scientific and technical potential (PPST).Authorisation to enter an area is granted by the director of the unit, following a favourable Ministerial decision, as defined in the decree of 3 July 2012 relating to the PPST. An unfavourable Ministerial decision in respect of a position situated in a ZRR would result in the cancellation of the appointment.
Recruitment Policy :
As part of its diversity policy, all Inria positions are accessible to people with disabilities.
Contacts
- Inria Team : SAIRPICO
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Recruiter :
Badoual Anais / anais.badoual@inria.fr
About Inria
Inria is the French national research institute dedicated to digital science and technology. It employs 2,600 people. Its 200 agile project teams, generally run jointly with academic partners, include more than 3,500 scientists and engineers working to meet the challenges of digital technology, often at the interface with other disciplines. The Institute also employs numerous talents in over forty different professions. 900 research support staff contribute to the preparation and development of scientific and entrepreneurial projects that have a worldwide impact.