Softwares

I build sofwares

I develop and contribute to softwares as part of my research work but also on my spare time. I release my softwares under Open Source license when it's possible. Most of my code is available on github at https://github.com/hadim.

kt_simul

A yeast mitosis simulation software created by Guillaume Gay, 2012. I have modified and used kt_simul during my PhD : https://github.com/bnoi/kt_simul.

spindle_tracker

A very specific Python module I daily use for my PhD project. It almost makes coffee : https://github.com/hadim/spindle_tracker.

Look at this code for example which convert a tiff file to a nicely annotated mp4 movie.

This module allows you to open in Python a Fiji/ImageJ binary ROI file.

PyGraphML

PyGraphML is a small library to parse GraphML files in Python : https://github.com/hadim/pygraphml.

scikit-tracker

scikit-tracker development has been stopped by Guillaume and me. Produced code has been included in our various specific and custom project.

scikit-tracker (http://scikit-tracker.org/) aims to be a robust Python library to work with cell biology microscopy images. OME Tiff is supported to handle input/output to the lib. The two main goals of the library is to implement detection and tracking algorithms relevant to analyse biological microscopy dataset.

This young project is developed by Guillaume Gay (http://damcb.com) and me. It is used to:

  • track chromosome trajectories during mitosis in fission yeast
  • track cell clusters displacement in D. melanogaster tissues

However we built scikit-tracker as a Python framework and it can be easily extended to meet to a wide range of problem encountered in cell biology.

Development is open (https://github.com/bnoi/scikit-tracker) which means that everyone can contribute to the code.

lsysdrawer

lsysdrawer is a software that allows visualizing L-system in 3D : https://github.com/hadim/lsysdrawer

profileextractor

profileextractor analizes and creates visualisation of segmented cells with http://www.cellprofiler.org. Visualisation has been strongly inspired from Collinet, 2010 (https://github.com/hadim/profileextractor).


I use softwares

I also actively use and contribute to Open Source softwares. Some of them are listed below.

  • python: interpreted, object-oriented, high-level programming language with dynamic semantics.
  • IPython : IPython is a command shell for interactive computing and data analysis.
  • matplotlib: python 2D plotting library which produces publication high quality figures.
  • numpy and scipy: mathematical library for python.
  • scikit-learn: machine learning python library.
  • scikit-image: image processing python library.
  • pandas: high-performance, easy-to-use data structures and data analysis tools for the python.
  • CellProfiler: easy and intuitive scientific images analysis.
  • ImageJ and Fiji: standard software in science to manipulate images in 2, 3, 4 and 5 dimensions.
  • Micro-Manager: open source software to control microscopes.
  • Vispy: high-performance interactive 2D/3D data visualization library.
  • trackpy: a Python particle tracking toolkit.
  • TrackMate: ImageJ plugin for single particle detection and tracking.