Community-developed checklists for publishing images and image analysis

Images document scientific discoveries and are prevalent in modern biomedical research. Microscopy imaging in particular is currently undergoing rapid technological advancements. However for scientists wishing to publish the obtained images and image analyses results, there are to date no unified guidelines. Consequently, microscopy images and image data in publications may be unclear or difficult to interpret. Here we present community-developed checklists for preparing light microscopy images and image analysis for publications. These checklists offer authors, readers, and publishers key recommendations for image formatting and annotation, color selection, data availability, and for reporting image analysis workflows. The goal of our guidelines is to increase the clarity and reproducibility of image figures and thereby heighten the quality of microscopy data is in publications.Comment: 28 pages, 8 Figures, 3 Supplmentary Figures, Manuscript, Essential recommendations for publication of microscopy image dat

Optimisation numérique et statistique pour la microscopie à éclairement structuré non contrôlé

Conventional structured illumination microscopy (SIM) can surpass the resolution limit inoptical microscopy caused by the diffraction effect, through illuminating the object with a set of perfectly known harmonic patterns. However, controlling the illumination patterns is a difficult task. Even worse, strongdistortions of the light grid can be induced by the sample within the investigated volume, which may give rise to strong artifacts in SIM reconstructed images. Recently, blind-SIM strategies were proposed, whereimages are acquired through unknown, non-harmonic,speckle illumination patterns, which are much easier to generate in practice. The super-resolution capacity of such approaches was observed, although it was not well understood theoretically. This thesis presents two new reconstruction methods in SIM using unknown speckle patterns (blind-speckle-SIM): one joint reconstruction approach and one marginal reconstruction approach. In the joint reconstruction approach, we estimate the object and the speckle patterns together by considering a basis pursuit denoising (BPDN) model with lp,q-norm regularization, with p=>1 and 01 et 0<q<=1. La norme lp,q est introduite afin de prendre en compte une hypothèse de parcimonie sur l’objet. Dans l’approche marginale, nous reconstruisons uniquement l’objet et les motifs d’éclairement sont traités comme des paramètres de nuisance. Notre contribution est double. Premièrement, une analyse théorique démontre que l’exploitation des statistiques d’ordre deux des données permet d’accéder à un facteur de super résolution de deux, lorsque le support de la densité spectrale du speckle correspond au support fréquentiel de la fonction de transfert du microscope. Ensuite, nous abordons le problème du calcul numérique de la solution. Afin de réduire à la fois le coût de calcul et les ressources en mémoire, nous proposons un estimateur marginal à base de patches. L’élément clé de cette méthode à patches est de négliger l’information de corrélation entre les pixels appartenant à différents patches. Des résultats de simulations et en application à des données réelles démontrent la capacité de super résolution de nos méthodes. De plus, celles-ci peuvent être appliquées aussi bien sur des problèmes de reconstruction 2D d’échantillons fins, mais également sur des problèmes d’imagerie 3D d’objets plus épais

A marginal image reconstruction approach in fluorescence microscopy with pseudo-random illumination patterns

International audienc

Minimum contrast estimation for super-resolution fluorescence microscopy using speckle patterns

National audienc

Fast reconstruction in blind fluorescence structured illumination microscopy

International audienc

Super-resolution capacity of imagers using random illuminations

International audienc

Super-resolution capacity of imagers using random illuminations

International audienc

Fast reconstruction in blind fluorescence structured illumination microscopy

International audienc

On the super-resolution capacity of imagers using unknown speckle illuminations

International audienc