Fractal tasks for the Opera/Operetta microscope and drug profiling
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Updated
Jul 7, 2024 - Python
Fractal tasks for the Opera/Operetta microscope and drug profiling
A collection of Image Processing and Analysis (IPA) functions used at the Facility for Advanced Imaging and Microscopy (FAIM)
Main tasks for the Fractal analytics platform
ITK IO for images stored in OME-Zarr format.
A lean and kind Open Microscopy Environment (OME) Next Generation File Format (NGFF) Zarr implementation.
Large-scale cell segmentation with cellpose.
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.
Course materials for the practical on the Defragmentation Training School 2 - Porto, 8-12 May 2023
Run encapsulated docker containers with BioFormats2Raw in the Amazon Web Services infrastructure.
Python code that I used in my blog posts on the Zarr file format.
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