Organizations: National Laboratory of Scientific Computinghttps://orcid.org/0000-0002-3811-4527
Teams: Not specified
Organizations: Not specifiedhttps://orcid.org/0000-0003-0429-2365
Hi! I'm Russell.
I'm a microbiologist who uses graph theory and machine learning to study the relationships that bacteria and archaea form with their host organisms, and lately giant viruses and their hosts. Or, I'm a computer scientist who builds software that uses concepts from evolution to extract knowledge about ecology from large datasets. Or, I'm a data scientist who uses Python to explore biological systems. Or, I'm a physicist that went rouge and defected to the squishy side of science. ...
Biomedical Engineer working on preclinical image dataset repository and cross researching RIs
Teams: Not specified
Organizations: Not specifiedhttps://orcid.org/0000-0001-6440-6980
I am a Ph.D. student in Gong lab. I am interested in cancer genomics, including the mining of genetic risk determinants in cancer, functional prediction of genetic variants, tumor-associated molecular epidemiology, large-scale data integration, analysis, and mining, as well as the construction of bioinformatical data platforms.
Teams: Not specified
Organizations: Not specifiedhttps://orcid.org/0000-0002-1399-293X
Dad, husband and PhD. Scientist, technologist and engineer. Bibliophile. Philomath. Passionate about science, medicine, research, computing and all things geeky!
Organizations: Pondicherry Universityhttps://orcid.org/0000-0003-4854-8238
Ph.D. Student at Department of Bioinformatics, Pondicherry University
Teams: MAB - ATGC
Organizations: Centre National de la Recherche Scientifique (CNRS)https://orcid.org/0000-0003-1590-8313
Name: Random Forest Contact Person: email@example.com Access Level: public License Agreement: Apache2 Platform: COMPSs Machine: MareNostrum4 This is an example of Random Forest algorithm from dislib. To show the usage, the code generates a synthetical input matrix. The results are printed by screen. This application used dislib-0.9.0
Submitter: Rutger Vos
Evaluation of Swin Transformer and knowledge transfer for denoising of super-resolution structured illumination microscopy data
In recent years, convolutional neural network (CNN)-based methods have shown remarkable performance in the denoising and reconstruction of super-resolved structured illumination microscopy (SR-SIM) data. Therefore, CNN-based architectures have been the main focus of existing studies. Recently, however, an alternative and highly competitive deep learning architecture, ...
MMV Im2Im Transformation
A generic python package for deep learning based image-to-image transformation in biomedical applications
The main branch will be further developed in order to be able to use the latest state of the art techniques and methods in the future. To reproduce the results of our manuscript, we refer to the branch ...
IDR is based on OMERO and thus all what we show in this notebook can be easily adjusted for use against another OMERO server, e.g. your institutional OMERO server instance.
The main objective of this notebook is to demonstrate how public resources such as the IDR can be used to train your neural network or validate software tools.
The authors of the PLOS Biology paper, "Nessys: A new set of tools for the automated detection of nuclei within intact tissues and dense 3D cultures" published in August ...
- Read data to analyse from an object store.
- Analyse data in parallel using Dask.
- Show how to use public resources to train neural network.
- Load labels associated to the original data
- Compare results with ground truth.
The authors of the PLOS Biology paper, "Nessys: A new set of tools for the automated detection of nuclei within intact tissues and dense 3D cultures" published in August 2019: https://doi.org/10.1371/journal.pbio.3000388, considered several image ...
- How to access genomic resource via its Python API
- How to access image resource via its Python API
- Relate image data to genomic data
Diabetes related genes expressed in pancreas
This notebook looks at the question Which diabetes related genes are expressed in the pancreas? Tissue and disease can be modified.
- Query humanmine.org, an integrated database of Homo sapiens genomic data using the intermine API to find the ...
The image is referenced in the paper "NesSys: a novel method for accurate nuclear segmentation in 3D" published August 2019 in PLOS Biology: https://doi.org/10.1371/journal.pbio.3000388 and can be viewed online in the Image Data Resource.
This original image was converted into the Zarr format. The analysis results produced by the authors of the paper were converted into labels and linked to the Zarr file which was placed into a public ...
A command line tool for converting image data into either of the standard file formats OME-TIFF or OME-Zarr.
The tool wraps the dedicated file converters bfconvert and bioformats2raw to convert into OME-TIFF or OME-Zarr, respectively. The workflow management system NextFlow is used to perform conversion in parallel for batches of images.
The tool also wraps s3 and Aspera clients (go-mc and aspera-cli, respectively). ...