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. https://omero.bio.fsu.edu/webclient/?show=dataset-5051
In addition they have also added a large dataset of both images and segmented images. https://omero.bio.fsu.edu/webclient/?show=project-2801
January 2021 Update: Hank Bass provides an overview to the INDEPTH Omero Repository. Download PDF.
Applications
The INDEPTH Image Repository has three main applications:
- Teaching datasets : for education purposes, e.g. – use in seminars, courses, lectures
- Training datasets : for software benchmarking
- 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- Unpublished images – kindly made available, under a confidentiality agreement for one or all of the three purposes mentioned above
Advantages
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)
Tutorials
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 |
|---|---|---|---|---|
| Project-2151 | Publication | 308 | DAPI staining, segmentation | Poulet et al (2015) Bioinformatics 31:1144-6 |
| Dataset-4151 | Publication | 2 | 3D-FISH | Rutowicz et al (2019) Genome Biology 20:157 |
 Project-2201 | Publication | 38 | DAPI-Hoechst staining, segmentation | Bilalovic et al (2020) Symmetry 12: 416 |
 Dataset-3008 | Publication | 38 | 3D FISH, STED images, RNA-FISH, nuclear GFP… | Dumur et al (2019) Nucleus 10: 181-212 |
| Dataset-4301 | Teaching | 11 | FISH, telomere, chromosome paint | Bass et al. (2000) Journal Cell Science 113:1149-1160. |
| 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
