Undergraduate, Master and Rotation Projects
The following Undergraduate, Master, or Rotation Ph.D. projects are available in the Strambio-De-Castillia lab. If you are interested, don't hesitate to Contact Us.
1) Development of Micro-Meta App advanced functionalities
One of the principal outputs of the Strambio-De-Castillia lab is the Micro-Meta App. This App was developed in the context of a global effort to improve reproducibility, data quality, and sharing value for imaging experiments. This community effort led to multiple publications featured on a recent Nature Methods FOCUS ISSUE dedicated to Reporting and reproducibility in microscopy.
Micro-Meta App is an intuitive, open-source software providing a visual interface for building comprehensive descriptions of the conditions used to produce microscopy datasets (including Hardware Specifications and Image Acquisition Settings) as specified by the 4DN-BINA-OME-QUAREP (NBO-Q) tiered system of Microscopy Metadata specifications, which expands the OME data model.
Multiple projects are available to improve the usability and efficiency of the Micro-Meta App microscopy metadata collection workflow. Please Contact Us for details.
Requirements: Experience with JavaScript is required. Familiarity with React is highly desirable.
2) Python scripts to automate pre-publication image data management and analysis in OMERO
OMERO is an integrated open-source client-server solution that provides a platform for annotating, organizing, visualizing, and analyzing image data. It can be used to build customized pipelines or integrate with existing applications to manage the complete pre-publication image-data life-cycle, including facilitating the sharing of data with colleagues and collaborators and making figures for publications.
Multiple projects are available to automate data management, metadata annotation and the integrated analysis of images stored in OMERO. Don't hesitate to Contact Us for details.
Requirements: Experience with Python is required.
3) Pipelines for Multiplexed FISH Chromatin Tracing data deposition, quality control, and sharing through the 4DN-Data Portal
A key output of the NIH-Common Fund 4D Nucleome (4DN) project is the open publication of datasets related to the structure of the human cell nucleus and the genome. Recent years have seen a rapid expansion of FISH-omics methods (aka Multiplexed FISH; reviewed in Dekker et al., 2023), which quantify the spatial organization of chromatin in single cells, sometimes together with RNA and protein measurements, and provide an expanded understanding of how 3D higher-order chromosome structure relates to transcriptional activity and cell development in both health and disease.
To empower the sharing, reuse, and downstream analysis of the results from FISH-omics experiments, the 4DN has led the development of FISH Omics Format for Chromatin Tracing (FOF-CT), a community-developed data standard for processed results deriving from a wide variety of Chromatin Tracing techniques. As a sign of broad adoption, 116 FISH Omics imaging datasets associated with 26 publications have been published to the 4DN Data Portal and the IDR repository.
Projects to develop automated pipelines to streamline the production and upload of FOF-CT datasets to public repositories are available. Contact Us for details.
Requirements: Advanced experience with Python is required.
4) Development of Next Generation Metadata frameworks compatible with OME-Zarr
For the past 15 years, there has been considerable momentum around efforts to foster the adoption of community metadata standards in light microscopy, including the launch of QUality Assessment and REProducibility for Images and Instruments in Light Microscopy (QUAREP-LiMi) global community of 600+ scientists and manufacturer representatives. With critical input from nine leading vendors, QUAREP-LiMi is launching the first-ever consensus metadata description of scientific-grade cameras to facilitate the transfer of essential hardware information to the community (Marx, 2022a; 2022b).
Thanks to the efforts described above, the time is optimal for the international microscopy community to develop a vendor-friendly OME-Zarr compatible framework named Next-Generation Framework for Metadata (NGM), a composable framework with user-friendly tools enabling the definition, capture, and exchange of community-specified metadata. For example, the NGM could be used to automatically transfer hardware-description metadata from instrument manufacturers to researchers.
Research projects are available to develop different aspects of the NGM framework of standard specifications and software tools. Don't hesitate to Contact Us for details.
Requirements: Advanced experience with Python is required. The candidate should also be familiar with the RDF, JSON-LD, and LinkML metadata standards of the World Wide Web Consortium (W3C).