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FilterFriend Public
A napari based tool for interactively setting filtering values for EASI-FISH spot detections
Python BSD 3-Clause "New" or "Revised" License UpdatedMar 6, 2026 -
fishspot Public
tools for finding discrete bright spots in images (for multiplexed FISH, includes background subtraction, deconv, and blob detection)
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cellpose Public
Forked from MouseLand/cellposea generalist algorithm for cellular segmentation
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lddmem Public
Large Deformation Diffeomorphic Metric Embedding: embed smooth deformable transforms from ANTs, Greedy, Elastix, CMTK etc. in the LDDMM framework.
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CircuitSeeker Public
Tools to help find neural circuits
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Parallel computing with task scheduling
Python BSD 3-Clause "New" or "Revised" License UpdatedMay 11, 2024 -
ossi-website Public
Forked from JaneliaSciComp/ossi-websiteWebsite showcasing projects supported through the Janelia Open Science Software Initiative (OSSI)
Astro BSD 3-Clause "New" or "Revised" License UpdatedApr 24, 2024 -
ngff-zarr Public
Forked from fideus-labs/ngff-zarrA lean and kind Open Microscopy Environment (OME) Next Generation File Format (NGFF) Zarr implementation.
Python MIT License UpdatedJul 19, 2023 -
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dask_stitch Public
Linear blend stitching for map_overlap calls in dask
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DECODE Public
Forked from TuragaLab/DECODEThis is the official implementation of our publication "Deep learning enables fast and dense single-molecule localization with high accuracy" (Nature Methods)
Python GNU General Public License v3.0 UpdatedMay 20, 2022 -
SpotGraph Public
Tools for dealing with smFISH spots and nuclei
Python MIT License UpdatedApr 25, 2022 -
dask-image Public
Forked from dask/dask-imageDistributed image processing
Python BSD 3-Clause "New" or "Revised" License UpdatedApr 1, 2022 -
air_localize_automation Public
Wrappers for AirLocalize in Python and BASH, for HPC
Python GNU General Public License v3.0 UpdatedFeb 17, 2022 -
awesome-janelia-software Public
Forked from JaneliaSciComp/awesome-janelia-softwareA curated list of awesome Janelia software
Creative Commons Zero v1.0 Universal UpdatedMay 25, 2021 -
SimpleITK Public
Forked from SimpleITK/SimpleITKSimpleITK: 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.
SWIG Apache License 2.0 UpdatedJan 23, 2021 -
greedypy Public
Greedy weak diffeomorphic image registration in Python
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closure-problem Public
Forked from hochbaumGroup/closure-problemTools for solving closure problems on graphs
Python Other UpdatedMay 22, 2020 -
HNCcorr Public
Forked from hochbaumGroup/HNCcorrHNCcorr algorithm for neuron identification in calcium imaging datasets.
Python Other UpdatedMay 22, 2020 -
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opencv Public
Forked from opencv/opencvOpen Source Computer Vision Library
C++ Other UpdatedApr 7, 2020 -
stardist Public
Forked from stardist/stardistStarDist - Object Detection with Star-convex Shapes
C BSD 3-Clause "New" or "Revised" License UpdatedMar 31, 2020 -
stream_old Public
Parallel deformable alignment of large N5 volumes using a cluster
Python GNU General Public License v3.0 UpdatedJan 31, 2020 -
regiprep Public
Preprocess confocal images for deformable registration.
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ANTs Public
Forked from ANTsX/ANTsAdvanced Normalization Tools (ANTs)
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pyrpl Public
PyRPL: Python Registration Prototyping Library. A Python package with deformable image registration algorithms, and modular components to build them.
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