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air_localize_automation

Wrappers for AirLocalize in Python and BASH, for HPC

ants

Advanced Normalization Tools (ANTs)

awesome-janelia-software

A curated list of awesome Janelia software

cellpose

a generalist algorithm for cellular segmentation

circuitseeker

Tools to help find neural circuits

closure-problem

Tools for solving closure problems on graphs

clusterwrap

Wrappers around dask-jobqueue functions for specific clusters

comp_methods_sca_module

dask

Parallel computing with task scheduling

dask-image

Distributed image processing

dask_stitch

Linear blend stitching for map_overlap calls in dask

decode

This is the official implementation of our publication "Deep learning enables fast and dense single-molecule localization with high accuracy" (Nature Methods)

fishspot

tools for finding discrete bright spots in images (for multiplexed FISH, includes background subtraction, deconv, and blob detection)

greedypy

Greedy weak diffeomorphic image registration in Python

hnccorr

HNCcorr algorithm for neuron identification in calcium imaging datasets.

img_register

lddmem

Large Deformation Diffeomorphic Metric Embedding: embed smooth deformable transforms from ANTs, Greedy, Elastix, CMTK etc. in the LDDMM framework.

napari-decode

Napari plugin for DECODE

ngff-zarr

A lean and kind Open Microscopy Environment (OME) Next Generation File Format (NGFF) Zarr implementation.

opencv

Open Source Computer Vision Library

ossi-website

Website showcasing projects supported through the Janelia Open Science Software Initiative (OSSI)

pyrpl

PyRPL: Python Registration Prototyping Library. A Python package with deformable image registration algorithms, and modular components to build them.

regiprep

Preprocess confocal images for deformable registration.

rnr-exm

simpleitk

SimpleITK: a layer built on top of the Insight Toolkit (ITK), intended to simplify and facilitate ITK's use in rapid prototyping, education and interpreted languages.

spotgraph

Tools for dealing with smFISH spots and nuclei

stardist

StarDist - Object Detection with Star-convex Shapes

stream_old

Parallel deformable alignment of large N5 volumes using a cluster