• Publié par : Denis CHRETIEN
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TubuleJ

Introduction

  • TubuleJ has been designed to facilitate the analysis of fiber and microtubule images obtained by transmission cryo-electron microscopy. It is composed of two modules: the first one can be used with any type of fiber, while the second is specific to microtubules.
  • The first module allows selection of fiber images, correction of grey level variations and straightening by automatic determination of their in plane curvature. Layer lines can be filtered in Fourier space to enhance specific helical families in the back transformed images. At present, we have tested successfully the straightening and filtering algorithms on microtubules, actin filaments and Tobacco Mosaic Virus (TMV) imaged by cryo-electron microscopy. We have also applied the straightening algorithm on stacks of images obtained by cryo-electron tomography.
  • The second module has been implemented to reconstruct in 3D microtubules with different protofilament and/or helical start numbers using a single particle approach. A stack of sub-images corresponding to the repetition and size of the basic motif is automatically extracted from the original curved or from the straightened version of the microtubule image. This stack  can be further processed by back projection to obtain a 3D reconstruction, which can be elongated to any size.
  • We are pleased to provide TubuleJ . Yet, we ask to not redistribute TubuleJ, but redirect interested users towards us for a new copy. This will help us to have a list of users, which will be useful if we need to apply for grants for further developments, and also to make sure that we provide the latest version available.
  • TubuleJ is provided with its code so that it can be freely modified. However, we would appreciate obtaining feedback when useful improvements have been performed. Also, please report any bug you may find.
  • Please quote the following reference in any publication that use TubuleJ:
  • A Fourier-based method for detecting curved microtubule centers: Application to straightening of cryo-electron microscope images
    Blestel, S., Kervrann, C., and D. Chrétien
    Proceedings of the IEEE International Symposium on Biomedical Imaging: From Nano to Macro, 2009. pp. 298-301.
    Web link
  • We would appreciate obtaining references of manuscripts that cite TubuleJ.
TubuleJ web site