Filter by OSSI funding status
An open-source platform for single-molecule localization
Develop a user-friendly (napari) deep learning-based single-molecule detection software.
Scientific Computing SoftwareTuraga LabPythonGPL-3.0PackageSingle-molecule localization microscopy (SMLM)Google ColabJupyter notebookLocal installationPyTorch
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 SoftwareJavaBSD-3 ClausePackageExpansion microscopy (ExM)Image registrationLightsheet fluorescence microscopy (LFSM)Spatial transcriptomicsLocal installationBigDataViewerFijiImgLib2Bioformats compatible formatsHDF5N5TIFFZARRZeiss CZI
BigStitcher-Spark
Run functionality of BigStitcher distributed on your workstation, a cluster or the cloud using Apache Spark.
Scientific Computing SoftwareJavaBSD-2 ClauseGPL-2.0Command line applicationExpansion microscopy (ExM)Image registrationLightsheet fluorescence microscopy (LFSM)Spatial transcriptomicsCloudHPC clusterLocal installationBigDataViewerImgLib2Bioformats compatible formatsHDF5N5TIFFZARR
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 LabMultiFISHScientific Computing SoftwareC++PythonBSD-3 ClauseFrameworkPackageAnnotationCalcium imagingConfocal light microscopy (LM)Correlative light EM (CLEM)Electron microscopy (EM)Expansion microscopy (ExM)Image registrationLightsheet fluorescence microscopy (LFSM)Single-molecule localization microscopy (SMLM)Spatial transcriptomicsCloudHPC clusterJupyter notebookLocal installationN5OME-ZarrTIFFZeiss CZI
BigWarp
Maintain and extend BigWarp (3D non-rigid registration for very large volumes).
Saalfeld LabJavaGPL-2.0Native applicationConfocal light microscopy (LM)Correlative light EM (CLEM)Electron microscopy (EM)Expansion microscopy (ExM)Image registrationLocal installationBigDataViewerFijiImgLib2Java Virtual MachineHDF5N5OME-ZarrTIFFZeiss CZI
Catena
Pipeline for automated connectome reconstruction from volume Electron Microscopy.
Cardona LabFunke LabScientific Computing SoftwarePythonAPACHEPackageElectron microscopy (EM)SegmentationTool packaging/distributionVisualizationHPC clusterLocal installationCUDANapariPyTorchTensorflowHDF5N5TIFFZARRCellpose
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 LabStringer LabPythonBSD-3 ClauseGPL-2.0PackageCalcium imagingConfocal light microscopy (LM)Electron microscopy (EM)Expansion microscopy (ExM)Google ColabLocal installationNapari
DaCapo
A framework for easy application of established machine learning techniques on large, multi-dimensional images.
CellMapFunke LabScientific Computing SoftwarePythonBSD-3 ClauseCommand line applicationFrameworkPackageConfocal light microscopy (LM)ConnectomicsCorrelative light EM (CLEM)Electron microscopy (EM)Expansion microscopy (ExM)Fluorescence microscopyLightsheet fluorescence microscopy (LFSM)SegmentationTool packaging/distributionCloudJupyter notebookLocal installationCUDANeuroglancerPyTorchN5OME-ZarrZARR
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.
FlyEMGoBSD-3 ClauseCommand line applicationFrameworkNative applicationServiceWeb applicationAnnotationConfocal light microscopy (LM)ConnectomicsData serviceElectron microscopy (EM)Expansion microscopy (ExM)SegmentationCloudLocal installationNeuroglancerNeuroglancer precomputed
EASI-FISH Pipeline
Automated analysis pipeline for EASI-FISH spatial transcriptomics data
MultiFISHScientific Computing SoftwareJavaMATLABNextflowPythonBSD-3 ClauseCommand line applicationExpansion microscopy (ExM)Spatial transcriptomicsCloudHPC clusterLocal installationBigDataViewerN5Zeiss CZI
Entrypoints
Support multiple entrypoint scripts in a container for use in containerized scientific tools.
Scientific Computing SoftwareGoBSD-3 ClauseCommand line applicationInfrastructureLocal installationFacemap
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 LabStringer LabPythonGPL-3.0Command line applicationGUI applicationPackageNeural recordingGoogle ColabJupyter notebookLocal installationavimpeg
Fileglancer
Browse, share, and publish OME-Zarr data.
Scientific Computing SoftwareJavascriptPythonTypescriptBSD-3 ClauseCommand line applicationPackageWeb applicationVisualizationHPC clusterLocal installationWeb browserNeuroglancerN5OME-ZarrZARR
GEFF - Graph Exchange File Format
A Python and Java compatible file format for exchanging graphs with annotated nodes and edges, with special support for tracking graphs.
Funke LabLive Image Tracking ToolsJavaPythonBSD-3 ClausePackageTrackingLocal installationFijiNapariN5OME-ZarrZARR
HortaCloud
Large volume volumetric rendering and collaborative neuron annotation in the cloud
MouseLightScientific Computing SoftwareJavaTypescriptBSD-3 ClauseNative applicationServiceWeb applicationWebsiteAnnotationExpansion microscopy (ExM)Lightsheet fluorescence microscopy (LFSM)CloudWeb browserJanelia WorkstationJava Virtual MachineOME-ZarrSWC
Java packaging tool chain
Develop an easy-to-use packaging system for Java applications.
Saalfeld LabScientific Computing SoftwareJavaServiceTool packaging/distributionLocal installationJava Virtual MachineKilosort
Maintain and develop python version of Kilosort (electrophysiology data).
Pachitariu LabStringer LabMATLABPythonGPL-2.0PackageElectrophysiologyNeural recordingGoogle ColabLocal installation
Maru
Maru is an opinionated command-line interface for quickly and easily containerizing scientific applications.
Scientific Computing SoftwareGoBSD-3 ClauseCommand line applicationInfrastructureLocal installationMotile Tracker
An application for interactive tracking with motile. Motile is a library that makes it easy to solve tracking problems using optimization by framing the task as an Integer Linear Program (ILP).
Funke LabScientific Computing SoftwarePythonBSD-3 ClauseCommand line applicationGUI applicationAnnotationConfocal light microscopy (LM)Fluorescence microscopyLightsheet fluorescence microscopy (LFSM)SegmentationTrackingVisualizationLocal installationNapariBioformats compatible formatsHDF5N5OME-ZarrTIFFZARR
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 SoftwareJavaJavascriptPythonBSD-3 ClauseServiceWeb applicationWebsiteConfocal light microscopy (LM)Electron microscopy (EM)CloudWeb browserH5JSWC
neuVid
Generates biology videos from high-level descriptions using Blender or VVD Viewer.
FlyEMScientific Computing SoftwarePythonCC-by-0Command line applicationNative applicationConfocal light microscopy (LM)Electron microscopy (EM)VisualizationLocal installationBlenderH5JOBJSWC
NIDAQ.jl
A Julia wrapper for National Instruments' driver
Scientific Computing SoftwareJuliaBSD-3 ClausePackageLocal installation
OSSI Website
A portfolio for projects supported by Open Science Software Initiative, and other software projects at Janelia
Scientific Computing SoftwareJavascriptBSD-3 ClauseWebsitePaintera
Annotation and Visualization of Large 3D Datasets with Paintera
Saalfeld LabJavaKotlinGPL-2.0Native applicationAnnotationElectron microscopy (EM)VisualizationLocal installationBigDataViewerImgLib2N5
Phase Diversity
Software for analyzing phase diversity data for adaptive optics
Shroff LabMATLABCC-by-4PackageFluorescence microscopyLocal installationTIFF
rastermap
A visualization method for neural data
Pachitariu LabStringer LabPythonGPL-3.0Command line applicationGUI applicationPackageAnnotationElectrophysiologyNeural recordingVisualizationJupyter notebookLocal installation
RS-FISH
Precise, interactive, fast, and scalable FISH spot detection
Scientific Computing SoftwareJavaGPL-2.0GPL-3.0Command line applicationFiji pluginFrameworkGUI applicationSequence analysisSpatial transcriptomicsCloudHPC clusterLocal installationBigDataViewerFijiImgLib2SparkBioformats compatible formatsN5ZARR
SongExplorer
deep learning for acoustic signals
Scientific Computing SoftwarePythonBSD-3 ClauseGUI applicationAnnotationSegmentationHPC clusterLocal installationTensorflowwav
Spatial Transcriptomics as Images Project (STIM)
A framework for storing, (interactively) viewing, and aligning spatial transcriptomics data.
Scientific Computing SoftwareJavaGPL-3.0Command line applicationFrameworkNative applicationSequence analysisSpatial transcriptomicsLocal installationBigDataViewerFijiImgLib2AnnDataN5Text files
Stitching-Spark
Reconstructing large microscopy images from overlapping image tiles on a high-performance Spark cluster.
Saalfeld LabJavaNextflowBSD-3 ClausePackageExpansion microscopy (ExM)Image registrationLightsheet fluorescence microscopy (LFSM)Spatial transcriptomicsCloudHPC clusterLocal installationBigDataViewerImgLib2N5TIFFZeiss CZISuite2p
Pipeline for processing two-photon calcium imaging data.
Pachitariu LabStringer LabPythonGPL-3.0PackageCalcium imagingNeural recordingGoogle ColabLocal installationNapari
Traccuracy
A library for evaluating cell tracking solutions against ground truth annotations.
Funke LabLive Image Tracking ToolsPythonBSD-3 ClausePackageTrackingLocal installation
TrainSpikingNet
train a spiking recurrent neural network
Scientific Computing SoftwareJuliaBSD-3 ClauseCommand line applicationCalcium imagingElectrophysiologyModellingNeural recordingHPC clusterLocal installationCUDA
Video Annotation Library
A usable and extensible video annotation library for machine learning
Branson LabScientific Computing SoftwareJavascriptPythonBSD-3 ClauseFrameworkPackageWeb applicationAnnotationCloudLocal installationWeb browseravimpeg
VVDViewer
Interactive 3D viewer/renderer for very large image volumes
Scientific Computing SoftwareC++BSD-3 ClauseNative applicationAnnotationConfocal light microscopy (LM)Electron microscopy (EM)Expansion microscopy (ExM)Local installationN5OME-ZarrSWCTIFFZARRZeiss CZI
x2s3
x2s3 is a service which can be used to provide an S3-compatible interface to any storage system. It powers s3.janelia.org.
Scientific Computing SoftwarePythonBSD-3 ClauseFrameworkServiceInfrastructureCloudWeb browserZarrcade
Zarrcade creates searchable web-based galleries of OME-Zarr images.
Scientific Computing SoftwarePythonBSD-3 ClauseWeb applicationWebsiteConfocal light microscopy (LM)Electron microscopy (EM)InfrastructureWeb browser