eLabFTW
Keep experiment notes, attachments, and shared lab records in a searchable browser workspace.
Lab SoftwareSelf-hosted web app
THE DIRECTORY
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Search by task, tool name, or collection.
124 tools
Benchling Notebook
Capture experiments in shared notebook pages and standardize repeated entries with lab templates.
Lab SoftwareHosted web app
Labguru
Connect experiment records, sample inventory, and equipment information in one lab workspace.
Lab SoftwareHosted web app
SciNote
Organize lab work into projects, experiments, and tasks, with shared notebook entries and inventory records.
Lab SoftwareHosted web app
RSpace
Connect a collaborative lab notebook to sample records and research data already stored elsewhere.
Lab SoftwareWeb app
protocols.io
Maintain versioned research methods and share an updated reference with colleagues or readers.
Lab SoftwareHosted web app
LabArchives ELN for Research
Keep searchable research notes, files, and shared notebook pages in a managed service.
Lab SoftwareHosted web app
Quartzy
Keep an inventory of lab supplies and track requests, approvals, and orders in a shared workspace.
Lab SoftwareHosted web app
Scanpy
Move from a single-cell expression matrix to quality checks, clusters, and exploratory plots in Python.
Single-cell AnalysisPython package
Seurat
Explore single-cell expression data in R, from initial filtering and clustering to comparisons across samples.
Single-cell AnalysisR package
CZ CELLxGENE Discover
Browse public single-cell datasets, inspect gene expression and cell annotations, or download data for follow-up analysis.
Single-cell AnalysisPublic data portal
scater
Inspect single-cell expression data with quality-control summaries, embeddings, and plots built around Bioconductor objects.
Single-cell AnalysisR package
SingleCellExperiment
Store expression matrices, gene and cell metadata, and embedding coordinates together in a standard R object.
Single-cell AnalysisR package
iSEE
Explore a prepared experiment in a browser with linked scatter plots, metadata tables, and expression views.
Single-cell AnalysisR / Shiny app
scDblFinder
Flag likely doublets, where a capture event contains more than one cell, before downstream interpretation.
Single-cell AnalysisR package
CellRank
Estimate candidate cell-state transitions and fate probabilities from processed single-cell observations.
Single-cell AnalysisPython package
Fiji
Open, inspect, and measure microscopy images in an ImageJ distribution that bundles common plugins.
Bioimage AnalysisDesktop app
QuPath
Annotate whole-slide images, measure objects, and export measurements from tissue image projects.
Bioimage AnalysisDesktop app
CellProfiler
Build reusable image-processing pipelines and export object measurements from batches of microscopy images.
Bioimage AnalysisDesktop app
napari
Explore multidimensional images, overlay segmentation masks, and edit annotations in interactive layers.
Bioimage AnalysisDesktop app / Python package
ilastik
Train image classifiers interactively by marking examples in a desktop interface, then export predictions for review.
Bioimage AnalysisDesktop app
OMERO
Store microscopy images and metadata in a central repository for viewing, organization, and controlled sharing.
Bioimage AnalysisServer / web app
Bio-Formats
Read image pixels and acquisition metadata from many microscope formats and export to formats such as OME-TIFF.
Bioimage AnalysisLibrary / plugin
TrackMate
Link detected objects across time-lapse frames and inspect or export the resulting trajectories.
Bioimage AnalysisFiji plugin
SciSure ELN
Record experimental work in a shared notebook with templates, attachments, and references to inventory.
Lab SoftwareHosted web app
LabCollector
Catalog samples, supplies, and equipment in configurable laboratory records.
Lab SoftwareWeb app
Labstep
Organize experimental records, shared methods, and inventory in a project workspace.
Lab SoftwareHosted web app
LabWare LIMS
Track laboratory samples, work assignments, review steps, and results through configured workflows.
Lab SoftwareEnterprise platform
LabVantage LIMS
Manage sample and test records in a browser-based laboratory information system.
Lab SoftwareEnterprise platform
Thermo Scientific SampleManager LIMS
Coordinate sample and result records, lab tasks, and review in one informatics platform.
Lab SoftwareEnterprise platform
Agilent SLIMS
Use a connected notebook and sample-management system to organize lab work and results.
Lab SoftwareEnterprise platform
Sapio LIMS
Build lab workflows that link sample records, task queues, and results.
Lab SoftwareEnterprise platform
LabKey Server Community Edition
Organize research datasets and collaborate around structured, permission-controlled records.
Lab SoftwareSelf-hosted web app
openBIS
Connect lab records and research datasets in a structured repository with project-level organization.
Lab SoftwareWeb app
SENAITE
Track sample reception, work queues, results, and review in a configurable LIMS.
Lab SoftwareSelf-hosted web app
OpenSpecimen
Track research specimens, aliquots, storage locations, and distributions.
Lab SoftwareWeb app
Freezerworks
Locate samples and aliquots in configured freezer layouts and manage inventory records.
Lab SoftwareLaboratory software
LabCup
Centralize laboratory inventories, storage locations, and shared equipment records.
Lab SoftwareHosted web app
Specify 7
Catalog biodiversity specimens, collection events, and associated records in a shared database.
Lab SoftwareWeb app
Agilent iLab
Coordinate core facility requests and equipment schedules in a common booking system.
Lab SoftwareHosted web app
QReserve
Make shared resources discoverable and manage reservations with local booking rules.
Lab SoftwareHosted web app
Calira
Schedule shared laboratory equipment and organize related lab operations in a common portal.
Lab SoftwareHosted web app
Calpendo
Book shared facility resources with configurable project rules and approvals.
Lab SoftwareHosted web app
LibreBooking
Give teams a browser calendar for reserving shared rooms, equipment, or other resources.
Lab SoftwareSelf-hosted web app
Meeting Room Booking System
Reserve meeting and instrument rooms in an uncomplicated shared calendar.
Lab SoftwareSelf-hosted web app
The Dataverse Project
Build a research data repository with dataset versions, metadata, and citations.
Lab SoftwareSelf-hosted web app
InvenioRDM
Deploy a configurable research repository for datasets, publications, and related records.
Lab SoftwareSelf-hosted web app
Zenodo
Deposit research outputs in a public repository and obtain a persistent identifier for released records.
Lab SoftwareHosted repository
Open Science Framework
Organize study materials, files, collaborators, and registrations in a research project workspace.
Lab SoftwareHosted web app
DataLad
Track dataset history and retrieve large file contents only when they are needed.
Lab SoftwareCommand-line tool
Data Version Control
Version data and record pipeline stages alongside the Git history for an analysis project.
Lab SoftwareCommand-line tool
Globus
Transfer and synchronize large research files between configured storage collections.
Lab SoftwareHosted service
REDCap
Build structured research data capture forms with validation and exports.
Lab SoftwareInstitutional web app
JupyterLab
Work with notebooks, files, terminals, and data views in a browser-based analysis environment.
Lab SoftwareNotebook environment
Quarto
Render research notes and code into reports, presentations, books, or websites.
Lab SoftwareCommand-line publishing tool
Snakemake
Run file-based analysis pipelines by declaring how each output depends on inputs and commands.
Lab SoftwareWorkflow engine
Nextflow
Describe data-processing steps and run the same workflow on supported local or remote computing backends.
Lab SoftwareWorkflow engine
renv
Record and restore a project-specific set of R package versions.
Lab SoftwareR package
AnnData
Keep a cell-by-feature matrix, annotations, and embeddings aligned in one object.
Single-cell AnalysisPython package
MuData
Organize modality-specific matrices and shared annotations together in a single container.
Single-cell AnalysisPython package
scvi-tools
Fit probabilistic models for tasks such as learning shared expression embeddings or transferring labels.
Single-cell AnalysisPython package
Squidpy
Summarize the arrangement of cells or spots in tissue with spatial neighbor graphs and coordinate-aware plots.
Single-cell AnalysisPython package
SpatialData
Keep expression tables, images, labels, and points in a common spatial data model.
Single-cell AnalysisPython package
Muon
Process measurements from separate modalities and combine their neighborhood information for exploratory analysis.
Single-cell AnalysisPython package
CellTypist
Assign provisional cell-type labels to RNA expression profiles using a selected pretrained classifier.
Single-cell AnalysisPython package
RAPIDS-singlecell
Run supported single-cell preprocessing and analysis steps on a GPU.
Single-cell AnalysisPython package
Cirrocumulus
Browse large expression datasets with linked embeddings, expression plots, and cluster composition views.
Single-cell AnalysisWeb visualization app
scVelo
Estimate RNA velocity to examine candidate directions of change among observed cell states.
Single-cell AnalysisPython package
DropletUtils
Read common droplet data formats and distinguish candidate cells from background droplets.
Single-cell AnalysisR package
batchelor
Reduce batch differences between expression datasets with methods including mutual nearest-neighbor correction.
Single-cell AnalysisR package
SingleR
Compare single-cell expression profiles with labeled references to suggest cell identities.
Single-cell AnalysisR package
celldex
Retrieve labeled expression references for human and mouse cell annotation.
Single-cell AnalysisR package
zellkonverter
Exchange H5AD expression data between Python's AnnData format and Bioconductor's SingleCellExperiment class.
Single-cell AnalysisR package
muscat
Test expression differences within annotated cell populations across samples, including pseudobulk analysis.
Single-cell AnalysisR package
miloR
Test for differences in cell abundance across graph neighborhoods without relying on a single partition into clusters.
Single-cell AnalysisR package
slingshot
Fit candidate branching trajectories through clusters and order cells along those trajectories.
Single-cell AnalysisR package
tradeSeq
Fit smooth gene expression trends along inferred trajectories and compare patterns between branches.
Single-cell AnalysisR package
dreamlet
Compare expression by cell type across cohorts, including designs with repeated samples.
Single-cell AnalysisR package
dittoSeq
Create configurable plots for expression, composition, and embeddings with colorblind-friendly palette options.
Single-cell AnalysisR package
Nebulosa
Overlay gene-weighted density on an embedding to show where expression from one or more features is concentrated.
Single-cell AnalysisR package
UCell
Score individual cells against predefined gene sets using expression ranks.
Single-cell AnalysisR package
SpatialExperiment
Keep spatial coordinates and image metadata aligned with expression assays in a Bioconductor object.
Single-cell AnalysisR package
scRNAseq
Load selected published single-cell count datasets and annotations into ready-to-analyze R objects.
Single-cell AnalysisR package
sctransform
Normalize UMI expression with a model that accounts for sequencing depth and stabilizes variation across genes.
Single-cell AnalysisR package
Harmony
Align single-cell datasets in a low-dimensional space while accounting for selected batch variables.
Single-cell AnalysisR package
scrapper
Use R interfaces to compiled routines for single-cell quality control, clustering, and marker summaries.
Single-cell AnalysisR package
Human Cell Atlas Data Explorer
Find Human Cell Atlas projects and inspect their sample, tissue, and file metadata.
Single-cell AnalysisPublic data portal
Broad Single Cell Portal
Explore public studies through interactive plots and retrieve the files their owners have made available.
Single-cell AnalysisPublic data portal
EMBL-EBI Single Cell Expression Atlas
Search single-cell expression studies across species and inspect gene expression patterns within individual experiments.
Single-cell AnalysisPublic data portal
UCSC Cell Browser
Open hosted datasets and color cell embeddings by gene expression or sample metadata.
Single-cell AnalysisPublic data portal
Allen Brain Cell Atlas
Browse reference brain cell expression and spatial data to compare annotated neural populations.
Single-cell AnalysisPublic data portal
Cellpose
Generate instance masks for cells or nuclei in microscopy images and inspect them in a graphical interface.
Bioimage AnalysisDesktop app / Python package
StarDist
Detect and segment individual nuclei and other compact objects using learned star-convex shapes.
Bioimage AnalysisPython package
InstanSeg
Run pretrained instance segmentation models on fluorescence or brightfield microscopy images to delineate cells and nuclei.
Bioimage AnalysisPython package / QuPath extension
μSAM
Prompt a microscopy segmentation model with points or boxes to outline objects and refine them interactively.
Bioimage Analysisnapari plugin / Python package
DeepImageJ
Run compatible pretrained models inside ImageJ for tasks such as microscopy segmentation or image restoration.
Bioimage AnalysisImageJ plugin
BigStitcher
Register and fuse tiled or multiview microscopy acquisitions to build a larger volume.
Bioimage AnalysisFiji plugin
BigDataViewer
Navigate large multiview volumes at several resolutions without loading the entire image into memory.
Bioimage AnalysisFiji plugin / Java library
MorphoLibJ
Apply mathematical morphology to clean masks, separate touching objects, and measure labeled structures in 2D or 3D.
Bioimage AnalysisImageJ plugin
CLIJ2
Run filtering, labeling, and measurement operations on an OpenCL-compatible GPU from Fiji workflows.
Bioimage AnalysisFiji plugin
BaSiCPy
Estimate and correct uneven illumination and background variation across microscopy images.
Bioimage AnalysisPython package
ModularImageAnalysis (MIA)
Assemble reusable image and object analysis workflows from modules for loading, segmentation, measurement, and output.
Bioimage AnalysisFiji plugin
OpenSlide
Read regions of multiresolution whole-slide images without loading the full slide.
Bioimage AnalysisLibrary / Python bindings
Slideflow
Extract tiles from whole-slide images and organize research workflows for model training and evaluation.
Bioimage AnalysisPython package
HistomicsTK
Process histology images with tools for stain handling, nuclei analysis, and feature extraction.
Bioimage AnalysisPython package
3D Slicer
Visualize, segment, and register volumetric images in an interactive research application.
Bioimage AnalysisDesktop app
ITK-SNAP
Inspect 3D image stacks and create segmentation masks using manual editing or semi-automatic tools.
Bioimage AnalysisDesktop app
Neuroglancer
Explore very large volumes, label layers, and meshes in a browser using multiresolution data sources.
Bioimage AnalysisBrowser viewer
CVAT Community Edition
Create and review image or video labels in a browser and export them for model development.
Bioimage AnalysisSelf-hosted web app
OME-Zarr Python
Read, write, and inspect OME-Zarr image pyramids and labels from a Python workflow.
Bioimage AnalysisPython package / CLI
BioIO
Load multidimensional microscopy images through format-specific readers and access their dimensions and metadata in Python.
Bioimage AnalysisPython package
scikit-image
Combine filtering, segmentation, morphology, and region measurement in array-based image analysis scripts.
Bioimage AnalysisPython package
SimpleITK
Apply image filtering and registration while retaining physical image geometry in scripted workflows.
Bioimage AnalysisPython / multi-language library
BioImage Archive
Search and download published biological imaging datasets with study metadata.
Bioimage AnalysisPublic data repository
Image Data Resource (IDR)
Browse curated imaging studies and their metadata in a public OMERO-based resource.
Bioimage AnalysisPublic image repository
Cytomine Community
Browse large biomedical images and collaborate on regions and annotations in browser-based projects.
Bioimage AnalysisSelf-hosted web app
Huygens
Restore microscopy images using deconvolution and inspect the results in a scientific imaging suite.
Bioimage AnalysisDesktop software suite
Imaris
Render 3D and time-series microscopy data, create objects, and quantify their geometry or motion.
Bioimage AnalysisDesktop software suite
Aivia
Build workflows for viewing, segmenting, and measuring multidimensional microscopy images with interactive tools.
Bioimage AnalysisDesktop software suite
ZEISS arivis Pro
Visualize large volumes and build repeatable image analysis pipelines for microscopy data.
Bioimage AnalysisDesktop software suite
Nikon NIS-Elements
Control supported Nikon image acquisition and organize or measure microscopy data within the same software family.
Bioimage AnalysisDesktop software suite
ZEISS ZEN
Acquire, view, and analyze microscopy images with modules matched to supported ZEISS instruments.
Bioimage AnalysisDesktop software suite
Dragonfly
Explore, segment, and measure 3D image volumes with interactive visualization and image-processing tools.
Bioimage AnalysisDesktop software suite
Image-Pro
Set up microscopy image analysis routines and aggregate measurements across image collections.
Bioimage AnalysisDesktop software suite
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