Author Archives: SergeDmi

Seplot : a simple command line (and python) plotting tool

Welcome seplot, a plotting tool to be used from the command line, or from a python script. It is a front-end for my favorite plotting program, PyX. To install it, just use : $ pip3 install seplot Then you can … Continue reading

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Simulations of Yeast Endocytosis

Video from In a paper published recently, we showed that actin nucleator are patterned on the membrane before and during the endocytic event. In particular, actin nucleators form a ring on the membrane around its attachment to the actin … Continue reading

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Internships available : 2018/2019

We have two internship opportunities available for a Master student for the university year 2018/2019. 1- Simulation of aster centering : Using an existing simulation engine, the student will seek to understand how microtubule properties (mechanics & dynamics) influence the … Continue reading

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Python command line tool for .ply files

I made a small python tool in order to convert/scale/align meshes stored in ply files. It is based around plyfile, a python module that read plyfiles and convert them to numpy arrays. It can also read/write from .mesh files, but … Continue reading

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Tools for statistics in Matlab

Science feels like reinventing the wheel each time. There are great statistics tools in Matlab but one needs the toolbox, even for a PCA… Of course this is free in python but since several pipelines are made in Matlab, I … Continue reading

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We’re hiring !

I am looking to hire a postdoctoral fellow in the topic of theoretical mechanics in biology. The advert is here :

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Simple command line plotting tool

I made a simple command line plotting tool : It’s available on my github To use it you should first install python PyX, a very nice plotting tool for python. PyX is great but sometimes you just want to … Continue reading

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Gamma distribution generator (and fitting) in Matlab… without toolboxes !

When working with confocal data, I found out that both noise and signal pixel value distribution could be very well fitted by a gamma distribution, with an offset. The pixel values were of the form Y=offset+X, where X is a … Continue reading

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The Cytosim music video

Every year, during “lab day” EMBL has a contest¬†of fun posters,¬† that depict the lab in a funny way, while mentioning the lab scientific activity. It is a great way to unleash one’s creativity while reaching out to the whole … Continue reading

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Generating confocal data from ideal signal

Left: cytosim simulation of a platelet marginal band. Right : simulated confocal stack. A large issue in image analysis is to make sure that the segmentation and analysis procedure does not create artifacts or misrepresents the data in any way. … Continue reading

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