Pinned Repositories
ANTs
Advanced Normalization Tools (ANTs)
cellpose
a generalist algorithm for cellular segmentation
CircuitSeeker
Tools to help find neural circuits
ClusterWrap
Wrappers around dask-jobqueue functions for specific clusters
dask_stitch
Linear blend stitching for map_overlap calls in dask
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
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
regiprep
Preprocess confocal images for deformable registration.
GFleishman's Repositories
GFleishman/CircuitSeeker
Tools to help find neural circuits
GFleishman/lddmem
Large Deformation Diffeomorphic Metric Embedding: embed smooth deformable transforms from ANTs, Greedy, Elastix, CMTK etc. in the LDDMM framework.
GFleishman/fishspot
tools for finding discrete bright spots in images (for multiplexed FISH, includes background subtraction, deconv, and blob detection)
GFleishman/greedypy
Greedy weak diffeomorphic image registration in Python
GFleishman/regiprep
Preprocess confocal images for deformable registration.
GFleishman/napari-decode
Napari plugin for DECODE
GFleishman/ANTs
Advanced Normalization Tools (ANTs)
GFleishman/cellpose
a generalist algorithm for cellular segmentation
GFleishman/ClusterWrap
Wrappers around dask-jobqueue functions for specific clusters
GFleishman/dask_stitch
Linear blend stitching for map_overlap calls in dask
GFleishman/Img_Register
GFleishman/pyrpl
PyRPL: Python Registration Prototyping Library. A Python package with deformable image registration algorithms, and modular components to build them.
GFleishman/air_localize_automation
Wrappers for AirLocalize in Python and BASH, for HPC
GFleishman/awesome-janelia-software
A curated list of awesome Janelia software
GFleishman/closure-problem
Tools for solving closure problems on graphs
GFleishman/comp_methods_sca_module
GFleishman/dask
Parallel computing with task scheduling
GFleishman/dask-image
Distributed image processing
GFleishman/DECODE
This is the official implementation of our publication "Deep learning enables fast and dense single-molecule localization with high accuracy" (Nature Methods)
GFleishman/HNCcorr
HNCcorr algorithm for neuron identification in calcium imaging datasets.
GFleishman/ngff-zarr
A lean and kind Open Microscopy Environment (OME) Next Generation File Format (NGFF) Zarr implementation.
GFleishman/opencv
Open Source Computer Vision Library
GFleishman/ossi-website
Website showcasing projects supported through the Janelia Open Science Software Initiative (OSSI)
GFleishman/rnr-exm
GFleishman/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.
GFleishman/SpotGraph
Tools for dealing with smFISH spots and nuclei
GFleishman/stardist
StarDist - Object Detection with Star-convex Shapes
GFleishman/stream_old
Parallel deformable alignment of large N5 volumes using a cluster