pr4deepr
Bioimage Analyst with a background in neuroscience and engineering. Particularly interested in Python, machine learning, data visualisation and analysis.
Walter and Eliza Hall Institute of Medical ResearchMelbourne, Australia
Pinned Repositories
napari_lattice
Napari plugin for custom analysis and visualization of lattice lightsheet and Oblique Plane Microscopy data. The plugin is optimized for data from the Zeiss lattice lightsheet microscope.
Australia_Victorian_crime_statistics
Crime statistics Victoria, Australia
calcium_background
cellpose-colab
Google Colab notebook for Cellpose
docker-example-omero
OMERO Docker compose example
GutAnalysisToolbox
Analysis and characterisation of cells within the gut wall using deep learning models. The current focus is on studying enteric neurons and enteric glia.
imagej_macros
Collection of ImageJ macros
read-roi
Read ROI files .zip or .roi generated with ImageJ.
smart_microscopy_minimal
Cut the cookie with Napari
visualising_enteric_glia_time_series
Using plotly to visualise activation of enteric glial cells (calcium imaging)
pr4deepr's Repositories
pr4deepr/cellpose-colab
Google Colab notebook for Cellpose
pr4deepr/GutAnalysisToolbox
Analysis and characterisation of cells within the gut wall using deep learning models. The current focus is on studying enteric neurons and enteric glia.
pr4deepr/docker-example-omero
OMERO Docker compose example
pr4deepr/smart_microscopy_minimal
Cut the cookie with Napari
pr4deepr/bg-atlasgen
pr4deepr/BiaPy
Open source Python library for building bioimage analysis pipelines
pr4deepr/cellpose
a generalist algorithm for cellular segmentation
pr4deepr/CLIc_prototype
GPU-accelerated Image Processing library
pr4deepr/COUNTEN
pr4deepr/czitools
This repository provides a collection of tools to simplify reading CZI (Carl Zeiss Image) pixel and metadata in Python. In addition it also contains other useful utilities to visualize CZI images inside Napari.
pr4deepr/DeepLabV3Plus-PyTorch
A DeepLab V3+ Model with ResNet 50 Encoder to perform Binary Segmentation Tasks. Implemented with PyTorch.
pr4deepr/DrLachie.github.io
pr4deepr/Folder-Structure-Conventions
Folder / directory structure options and naming conventions for software projects
pr4deepr/imagej-updater
The automatic updater for ImageJ
pr4deepr/imagej.github.io
The ImageJ wiki
pr4deepr/kaggle-solutions
🏅 Collection of Kaggle Solutions and Ideas 🏅
pr4deepr/list-of-update-sites
The update sites ImageJ knows about automatically
pr4deepr/MESmerize
Platform for Calcium Imaging analysis
pr4deepr/napari-aicsimageio
Multiple file format reading directly into napari using pure Python
pr4deepr/napari-workflows
pr4deepr/NoCodeSeg
🔬 Code-free deep segmentation for computational pathology
pr4deepr/npy2bdv
Fast writing of numpy 3d-arrays into HDF5 Fiji/BigDataViewer files.
pr4deepr/OAD
Collection of tools and scripts useful to automate microscopy workflows in ZEN Blue using Python and Open Application Development tools.
pr4deepr/plant-seg
A tool for cell instance aware segmentation in densely packed 3D volumetric images
pr4deepr/pr4deepr
Profile README
pr4deepr/pyclesperanto
GPU-accelerated Image Processing library using OpenCL
pr4deepr/pyclesperanto_prototype
http://clesperanto.net
pr4deepr/rse-aunz.github.io
https://rse-aunz.github.io/
pr4deepr/RSEAA.github.io
Website and project management for RSEAA2023
pr4deepr/tifffile
Read and write TIFF files. Forked from https://pypi.org/project/tifffile