A nextflow based tool that wraps bfconvert and bioformats2raw to convert image data collections to OME-TIFF and OME-Zarr, respectively, in a parallelised manner.
A Python-based tool for parallelized conversion of image datasets from various formats to OME-Zarr, with support for distributed processing and multi-dimensional concatenation.
Course materials for the practical on the Defragmentation Training School 2 - Porto, 8-12 May 2023
Bio- and biomedical imaging dataset for machine learning and deep learning (for ExperimentHub in Bioconductor)
Jupyter Notebooks e codigos para analise de bioimagens e dados biologicos utilizados no meu canal BioPrograma - https://www.youtube.com/channel/UCbJAU7N9FYvwkdgSwD_1S4Q
Automated analysis of brain tissue images using Python (GFAP, SOX9, NeuN, Hoechst)
A specialized batch-processing pipeline for Zeiss CZI files. Optimized for ApoTome & Brain sections. Fixes hyperstack dimensions, recovers LUTs, and removes shading via rolling-ball pre-processing.
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