eLabFTW
Keep experiment notes, attachments, and shared lab records in a searchable browser workspace.
Lab SoftwareSelf-hosted web app
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24 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
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