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An open-source platform for single-molecule localization
Develop a user-friendly (napari) deep learning-based single-molecule detection software.
Scientific Computing Software Turaga Lab Python GPL-3.0 Package Single-molecule localization microscopy (SMLM) Google Colab Jupyter notebook Local installation PyTorch
BigStitcher-Spark
Run functionality of BigStitcher distributed on your workstation, a cluster or the cloud using Apache Spark.
Scientific Computing Software Java BSD-2 Clause GPL-2.0 Command line application Expansion microscopy (ExM) Image registration Lightsheet fluorescence microscopy (LFSM) Spatial transcriptomics Cloud HPC cluster Local installation BigDataViewer ImgLib2 Bioformats compatible formats HDF5 N5 TIFF ZARR
BigStitcher
A software package that allows simple and efficient alignment of multi-tile and multi-angle image datasets, for example acquired by lightsheet, widefield or confocal microscopes.
Scientific Computing Software Java BSD-3 Clause Package Expansion microscopy (ExM) Image registration Lightsheet fluorescence microscopy (LFSM) Spatial transcriptomics Local installation BigDataViewer Fiji ImgLib2 Bioformats compatible formats HDF5 N5 TIFF ZARR Zeiss CZI
BigStream
Flexible and powerful image registration tools for small and big data (TB+) alike. Stitching, subject-to-atlas, multi-modal, in vivo to ex vivo, and motion correction. 100% Python, can be run from Jupyter notebooks, including full access to workstation or adaptable distributed resources.
Ahrens Lab MultiFISH Scientific Computing Software C++ Python BSD-3 Clause Framework Package Annotation Calcium imaging Confocal light microscopy (LM) Correlative light EM (CLEM) Electron microscopy (EM) Expansion microscopy (ExM) Image registration Lightsheet fluorescence microscopy (LFSM) Single-molecule localization microscopy (SMLM) Spatial transcriptomics Cloud HPC cluster Jupyter notebook Local installation N5 OME-Zarr TIFF Zeiss CZI
BigWarp
Maintain and extend BigWarp (3D non-rigid registration for very large volumes).
Saalfeld Lab Java GPL-2.0 Native application Confocal light microscopy (LM) Correlative light EM (CLEM) Electron microscopy (EM) Expansion microscopy (ExM) Image registration Local installation BigDataViewer Fiji ImgLib2 Java Virtual Machine HDF5 N5 OME-Zarr TIFF Zeiss CZICatena
Pipeline for automated connectome reconstruction from volume Electron Microscopy.
Cardona Lab Funke Lab Scientific Computing Software Python APACHE Package Electron microscopy (EM) Segmentation Tool packaging/distribution Visualization HPC cluster Local installation CUDA Napari PyTorch Tensorflow HDF5 N5 TIFF ZARR
Cellpose
A generalist algorithm for cell and nucleus segmentation (v1.0) that can be optimized for your own data (v2.0) and perform image restoration (v3.0).
Pachitariu Lab Stringer Lab Python BSD-3 Clause GPL-2.0 Package Calcium imaging Confocal light microscopy (LM) Electron microscopy (EM) Expansion microscopy (ExM) Google Colab Local installation Napari
DaCapo
A framework for easy application of established machine learning techniques on large, multi-dimensional images.
CellMap Funke Lab Scientific Computing Software Python BSD-3 Clause Command line application Framework Package Confocal light microscopy (LM) Connectomics Correlative light EM (CLEM) Electron microscopy (EM) Expansion microscopy (ExM) Fluorescence microscopy Lightsheet fluorescence microscopy (LFSM) Segmentation Tool packaging/distribution Cloud Jupyter notebook Local installation CUDA Neuroglancer PyTorch N5 OME-Zarr ZARR
DVID
A dataservice for branched versioning of a variety of data types including teravoxel-scale image volumes, sparse volumes, meshes, and JSON and point annotations.
FlyEM Go BSD-3 Clause Command line application Framework Native application Service Web application Annotation Confocal light microscopy (LM) Connectomics Data service Electron microscopy (EM) Expansion microscopy (ExM) Segmentation Cloud Local installation Neuroglancer Neuroglancer precomputed
EASI-FISH Pipeline
Automated analysis pipeline for EASI-FISH spatial transcriptomics data
MultiFISH Scientific Computing Software Java MATLAB Nextflow Python BSD-3 Clause Command line application Expansion microscopy (ExM) Spatial transcriptomics Cloud HPC cluster Local installation BigDataViewer N5 Zeiss CZIEntrypoints
Support multiple entrypoint scripts in a container for use in containerized scientific tools.
Scientific Computing Software Go BSD-3 Clause Containerization
Facemap
A framework for predicting neural activity from mouse orofacial movements. It includes a pose estimation model for tracking distinct keypoints on the mouse face, a neural network model for predicting neural activity using the pose estimates, and also can be used compute the singular value decomposition (SVD) of behavioral videos.
Pachitariu Lab Stringer Lab Python GPL-3.0 Command line application GUI application Package Neural recording Google Colab Jupyter notebook Local installation avi mpeg
HortaCloud
Large volume volumetric rendering and collaborative neuron annotation in the cloud
MouseLight Scientific Computing Software Java Typescript BSD-3 Clause Native application Service Web application Website Annotation Expansion microscopy (ExM) Lightsheet fluorescence microscopy (LFSM) Cloud Web browser Janelia Workstation Java Virtual Machine OME-Zarr SWCJava packaging tool chain
Develop an easy-to-use packaging system for Java applications.
Saalfeld Lab Scientific Computing Software Java Service Tool packaging/distribution Local installation Java Virtual Machine
Kilosort
Maintain and develop python version of Kilosort (electrophysiology data).
Pachitariu Lab Stringer Lab MATLAB Python GPL-2.0 Package Electrophysiology Neural recording Google Colab Local installationMaru
Maru is an opinionated command-line interface for quickly and easily containerizing scientific applications.
Scientific Computing Software Go BSD-3 Clause Containerization
NeuronBridge
A web application for easily and rapidly finding putative morphological matches between large data sets of neurons imaged using different modalities, namely electron microscopy (EM) and light microscopy (LM). Matches have been precomputed for all of Janelia's public EM/LM data sets, and are quick to look up by identifier. You can also upload your own data and match it against these public data sets.
Scientific Computing Software Java Javascript Python BSD-3 Clause Service Web application Website Confocal light microscopy (LM) Electron microscopy (EM) Cloud Web browser H5J SWC
neuVid
Generates biology videos from high-level descriptions using Blender or VVD Viewer.
FlyEM Scientific Computing Software Python CC-by-0 Command line application Native application Confocal light microscopy (LM) Electron microscopy (EM) Visualization Local installation Blender H5J OBJ SWC
NIDAQ.jl
A Julia wrapper for National Instruments' driver
Scientific Computing Software Julia BSD-3 Clause Package Local installationOSSI Website
A portfolio for projects supported by Open Science Software Initiative, and other software projects at Janelia
Scientific Computing Software Javascript BSD-3 Clause Website
Paintera
Annotation and Visualization of Large 3D Datasets with Paintera
Saalfeld Lab Java Kotlin GPL-2.0 Native application Annotation Electron microscopy (EM) Visualization Local installation BigDataViewer ImgLib2 N5
Phase Diversity
Software for analyzing phase diversity data for adaptive optics
Shroff Lab MATLAB CC-by-4 Package Fluorescence microscopy Local installation TIFF
RS-FISH
Precise, interactive, fast, and scalable FISH spot detection
Scientific Computing Software Java GPL-2.0 GPL-3.0 Command line application Fiji plugin Framework GUI application Sequence analysis Spatial transcriptomics Cloud HPC cluster Local installation BigDataViewer Fiji ImgLib2 Spark Bioformats compatible formats N5 ZARR
SongExplorer
deep learning for acoustic signals
Scientific Computing Software Python BSD-3 Clause GUI application Annotation Segmentation HPC cluster Local installation Tensorflow wav
Spatial Transcriptomics as Images Project (STIM)
A framework for storing, (interactively) viewing, and aligning spatial transcriptomics data.
Scientific Computing Software Java GPL-3.0 Command line application Framework Native application Sequence analysis Spatial transcriptomics Local installation BigDataViewer Fiji ImgLib2 AnnData N5 Text filesStitching-Spark
Reconstructing large microscopy images from overlapping image tiles on a high-performance Spark cluster.
Saalfeld Lab Java Nextflow BSD-3 Clause Package Expansion microscopy (ExM) Image registration Lightsheet fluorescence microscopy (LFSM) Spatial transcriptomics Cloud HPC cluster Local installation BigDataViewer ImgLib2 N5 TIFF Zeiss CZI
Suite2p
Pipeline for processing two-photon calcium imaging data.
Pachitariu Lab Stringer Lab Python GPL-3.0 Package Calcium imaging Neural recording Google Colab Local installation Napari
TrainSpikingNet
train a spiking recurrent neural network
Scientific Computing Software Julia BSD-3 Clause Command line application Calcium imaging Electrophysiology Modelling Neural recording HPC cluster Local installation CUDA
Video Annotation Library
A usable and extensible video annotation library for machine learning
Branson Lab Scientific Computing Software Javascript Python BSD-3 Clause Framework Package Web application Annotation Cloud Local installation Web browser avi mpeg
VVDViewer
Interactive 3D viewer/renderer for very large image volumes
Scientific Computing Software C++ BSD-3 Clause Native application Annotation Confocal light microscopy (LM) Electron microscopy (EM) Expansion microscopy (ExM) Local installation N5 SWC TIFF Zeiss CZI