Category Archives: Code

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

From left to right : ground truth (projected), mock confocal image (projected) and thresholded pixels. 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 … Continue reading

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Spindle analysis GUI

In the article “Spindle assembly on immobilized chromatin micropatterns”, we observe reconstituted meiosis spindles in live microscopy. This our method generates a large set of data, with many spindles, the dynamics of which we want to quantify. For this, I developed … Continue reading

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Python utilities

I decided to upload my most commonly used Python utilities to Github. : https://github.com/SergeDmi/Python-Tools You’ll find there : Reading/writing array from/to file Running bash jobs from python and returning output File text cleanup and parsing And a bit more…

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