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agrifieldnet

My messy attempt at the AgriFieldNet India Challenge (https://zindi.africa/competitions/agrifieldnet-india-challenge). Crop classification with Transformers

am_utils

Some useful functions

awesome-climate-change

A collection of awesome resources about climate change.

biomassters

The BioMassters challenge (https://www.drivendata.org/competitions/99/biomass-estimation/page/534/)

care_batch

Batch restoration with CARE

cellfinder

Automated 3D cell detection and registration of whole-brain images

cosmos-care

COSMOS recipe for CARE

cs-net

CS-Net (MICCAI 2019) and CS2-Net (MedIA 2020)

cs-sim

Synthetic images with curvilinear structures; 2D and 3D.

csnet

Re-implementation of the original CS-Net (https://github.com/iMED-Lab/CS-Net) using MONAI (https://github.com/Project-MONAI/MONAI).

deconvtest

A python-based simulation framework that allows the user to quantify and compare the performance of different deconvolution methods.

deconvtest2

Optimized version of DeconvTest: framework to quantify and compare the performance of image restoration methods

filament_annotator_3d

Annotation of filament / curvilinear structures in 3D based on napari viewer

helperlib

Helper functions for working with files and parallel processing

images_for_cellpose_issue

test images for cellpose issue: https://github.com/MouseLand/cellpose/issues/225

intake_io

Image-focused IO for Python using intake and xarray

ml_utils

code for object detection training

napari-filament-annotator

Annotation of filaments and other curvilinear structures in 3D.

naparimovie

Create movies from series of key-frames in napari.

pretty-print-confusion-matrix

plot a pretty confusion matrix with seaborn and matplotlib in python

trace-net