• INDEPTH Image Repository

  • WG1_Image_Arabidopsis_nucleus_DNA_STED-_image-Dr-Ricardo-Randall_

    Advances in imaging technologies allow the plant nucleus to be analysed in incredible detail.

    INDEPTH is promoting the use of an image repository of 3D images of plant nuclei. This initiative is focused on the 3D images acquired by INDEPTH members and we hope will contribute to enhancing the visibility of imaging excellence in plant science.

    The INDEPTH Image Repository is an open access facility to benefit the plant science community. This is hosted on the OMERO servers at Florida State University (Curator- Hank Bass).

    December 2020 Update: Tristan Dubos, Sophie Desset and Christophe Tatout have uploaded a training dataset of wide-field images of 114 nuclei to use with their new NucleusJ 2.0 publication

    In addition they have also added a large dataset of both images and segmented images.

    January 2021 Update: Hank Bass provides an overview to the INDEPTH Omero Repository. Download PDF.


    The INDEPTH Image Repository has three main applications:

    1.      Teaching datasets : for education purposes, e.g. - use in seminars, courses, lectures 

    2.      Training datasets : for software benchmarking

    3.      Sharing knowledge with collaborators: to facilitate collaboration and data sharing. 

     Open Access

     The repository is a two-way facility where users can access the images and can also submit images for inclusive.

    The INDEPTH Image Repository welcomes the submission of: 

    • Published images - a link/DOI provided in a publication to a repository enabling the open access to all image data allowing  a better access to publish data, a better visibility of Plant database). Ultimately published images will be transferred on IDR (  OMERO-based)
    • Unpublished images - kindly made available, under a confidentiality agreement for one or all of the three purposes mentioned above


    The INDEPTH image repository offers advantages such as:

    • A way to store 3D images from plants
    • A link/DOI provided in a publication to a repository enabling the open access to all image data (allow a better access to publish data, a better visibility of Plant database)
    • A good resource for teaching (meiosis, cell cycle, replication…)
    • A good resource for software benchmarking
    • It optimizes longevity, reusability, reanalysis of image data 
    • A way to share knowledge and information about experiments underlying the images 
    • A compatible format with IDR general repository (all organisms)


    Please download a How-to-Use guide for the OMERO repository as well as watching this Introductory video:


     List of Resources

    Below is a list of all the images that are currently included in the INDEPTH OMERO repository

     Web Link  Source  Number of Images  Technique  Description
    WG1_2151 Project-2151  Publication  308  DAPI staining, segmentation   Poulet et al (2015) Bioinformatics 31:1144-6
    WG1_4151 Dataset-4151  Publication  2  3D-FISH   Rutowicz et al (2019) Genome Biology 20:157
    WG1_2201  Project-2201  Publication  38  DAPI-Hoechst staining, segmentation   Bilalovic et al (2020) Symmetry 12: 416
    WG1_3008  Dataset-3008  Publication  38  3D FISH, STED images, RNA-FISH, nuclear GFP...   Dumur et al (2019) Nucleus 10: 181-212
    WG1_4301_ Dataset-4301   Teaching  11  FISH, telomere, chromosome paint   Bass et al. (2000) Journal Cell Science 113:1149-1160.
    WG1_4101_ Dataset-4101   Teaching  28  DNA replication EdU-A488   Bass et al. (2015) Plant Mol Biol 89:339

    The numbering/content scheme used on the OMERO database:

    IDP1000-1999 for TEACHING 

    IDP2000-2999 for TRAINING

    IDP3000-3999 for PUBLICATIONS

    IDP4000-4999 for UNPUBLISHED

    Nucleus animation credits:  R. Randall and C.Baroux, University of Zürich

  • Joining the INDEPTH COST Action

    If you are interested in joining Action please contact the INDEPTH Chairman stating why the research program of your lab would enhance the overall activity of the Action.

    Christophe Tatout