Replicative aging of budding yeast
Device to trap single budding yeast cells and track them throughout their replicative lifespan. Publication
Single-cell isolation and observation for mammal cells
Device to trap single mammal cells, submit them to drugs and perform timelapse movies. Was successfully used with mouse ES cell line.
S. pombe and S. cerevisiae clonal aging
Device to trap single fission yeast cells and track them throughout their divisions. Can also be used to study clonal replicative aging in budding yeast (telomerase-deficient cells), with the daughter frequently replacing the mother in the trap.
Continuous filtration of cells
Device to separate cells from the media in a continuous manner. Works with budding and fission yeast but can be adapted to work with cells of a different size. Publication, Detailed protocol
In-chip harvestable cell culture
One key aspect of microfluidics is the control of the environment and its dynamics. However, cells in microfludic devices are difficult to retrieve or require a complex secondary fluidic system. I developed this device that allows to stress an in-chip culture with any stress dynamics (ramp, short steps, ...), before harvesting it for subsequent assays. It is optimized for budding yeast, but could work with other non-adherent cells that are not sensitive to mild mechanical stress.
C. elegans observation
Device to immobilize C. elegans worms, submit them to drugs or perform timelapse movies. Publication
Particle filter
Simple device to filter particles above a certain size by trapping them in PDMS microstructures. Typically used to filter out dust or debris upstream of a critical microfluidic device. Publication
DetecDiv
DetecDiv is a MATLAB-based software developed by Gilles Charvin and myself to track large numbers of single cells in different contexts. For example, it can be used to automatically detect cell divisons and segment cell bodies, using deep-learning networks. It is particularly efficient when used on timelapse images of cells in microfluidics traps. DetecDiv also includes a GUI and a set of functions for data visualisation, manual annotation, plotting and export (figures, movies...)(See publication.)
HeatChips: a microfluidic heating device
HeatChips is a simple, cost-effective system to heat samples inside PDMS-based microfluidic devices in a homogeneous manner. It is based on a transparent heating glass in contact with the top of the microfluidic device, and a contactless, infrared temperature sensor attached to the objective that directly reads the temperature of the bottom of the chip. This portable system is compatible with most chip designs and allows imaging of the sample on inverted microscopes for extended periods of time without any optical restriction, for a cost of less than 100€.
3D printing
Some of my designs: 
Micromanager scripts, control of pumps and valves
My micromanager pluggins and scripts
Matlab software to control ISMATEC Pumps
DeepFluidics, a home-made programmable multiplexer with 8 independant valves
Communities, resources and softwares
Microphysiological systems, Organ-on-chip, organoids
BaCell3D: Conference on building advanced multiCellular systems in 3D
GDR Organoids: French network about organoids and organ-on-chip
EUROoCS: European Organ-on-Chip Society
UK Organ-on-a-Chip Technologies Network
ITB: Institute for Translational Bioengineering
IBEC: Institute for Bioengineering of Catalonia
FSSCR: French Society for Stem Cell Research
CSEM: Swiss Center for Electronics and Microtechnics
Microfluidics, microfabrication, 3D design and hardware
GDR MNF: French network about micro and nano fluidics
"Chips and Tips" blog of the Royal society of chemistry: Resource describing useful micro and macrofluidic devices and tips.
Metafluidics: Open repository for microfluidic systems
COMSOL: powerful software to simulate physics, and in particular microfluidics mecanics, useful for pre-prototyping.
AutoCAD: powerful software for 2D CAD designs.
Fusion360: powerful software for 3D designs.
Thingiverse, Cults3D and NIH 3D Print Exchange: online repositories for 3D printing designs.
Open Hardware Repository: the GitHub of hardware.
Microscopy
Micromanager: free and open-source software for the control and automation of microscopy-related hardwares.
Image.sc: forum gathering the microscopy and image analysis community.
Microlist: database gathering information about the microscopy & image analysis community: conferences, courses, softwares and tools.
GDR ImaBio: French network about imaging and image analysis
GDR AGV: French network about quantitative biology
AI and biodata analysis
Deep learning with Python (2nd edition): a very comprehensive book from François Chollet.
3Blue1Brown and StatQuest: Youtube channels for an introduction to stats and machine learning.
TowardsDataScience: Community articles about AI and data science.
Bioimage.io and Modelzoo.co: repository to upload trained machine learning networks as well as annotated datasets.
Paperswithcode.com: repository to upload trained machine learning networks as well as annotated datasets.
List of AI-powered tools for productivity and art.