Today, AdvaitaBio is launching iSCanGuide v3.0, a major new release designed to help researchers analyze single-cell and spatial transcriptomics data at a scale that has often been slow, fragmented, and difficult to manage. With support for projects spanning hundreds of samples and tens of millions of cells, iSCanGuide v3.0 brings interactive, GPU-accelerated analysis to workflows that used to demand significant time, infrastructure, and computational expertise.
This launch is about more than performance alone. It changes what researchers can do in the moment. Instead of breaking analysis into disconnected steps across multiple tools, teams can move through a guided, end-to-end workflow with more speed, more continuity, and clearer analytical provenance.
What Is New in iSCanGuide v3.0
iSCanGuide v3.0 introduces a more launch-ready environment for large-scale single-cell and spatial analysis. The release brings together the core steps researchers need to move from raw or processed data to interpretable biological results inside one connected platform.
- Interactive analysis for studies spanning hundreds of samples and tens of millions of cells.
- A redesigned user experience that keeps QC, analysis, and visualization connected.
- AI-powered atlas-level annotation support with CellTypist and Geneformer.
- Trajectory analysis with StaVia for spatial or large datasets and Slingshot for smaller non-spatial studies.
- Built-in provenance that keeps every major analytical step trackable, shareable, and reproducible.
Why This Release Matters Right Now
Single-cell and spatial transcriptomics studies are moving faster and getting larger, but many workflows still depend on disconnected tools, repeated exports, and specialist intervention. As datasets scale, those gaps become harder to ignore.
iSCanGuide v3.0 is built for that moment. It gives researchers a more direct path from data to interpretation, helping teams spend less time on workflow overhead and more time generating biological insight.
What This Launch Means for Experienced Researchers
For experienced researchers, iSCanGuide v3.0 creates a faster way to iterate on large analyses without losing rigor. The release keeps major analytical steps connected, making it easier to test ideas, compare outputs, and revisit decisions inside one environment.
Faster Iteration Across the Same Workflow
iSCanGuide v3.0 keeps QC, embedding, clustering, annotation, differential expression, enrichment, cell-cell communication, trajectory inference, and spatial analysis inside one GPU-accelerated platform. That makes it easier to evaluate downstream effects after adjusting upstream choices, without breaking context between separate systems.
For teams working through exploratory analysis, that speed can make a meaningful difference. You can test clustering strategies, compare annotation outputs, and refine decisions while keeping the full workflow connected.
Reproducibility That Stays Attached to the Work
iSCanGuide v3.0 also strengthens reproducibility through built-in provenance. Filtering choices, analytical parameters, and result lineage remain tied to the outputs they generate, giving teams a clearer record of what was done and how conclusions were reached.
What This Launch Means for Researchers Without Deep Computational Expertise
For researchers who know the biology but do not want every project to depend on code, specialized infrastructure, or constant support, iSCanGuide v3.0 makes independent analysis more practical.
More Independence With Less Delay
Because iSCanGuide is guided and GUI-driven, researchers can move through standard workflows without writing code. Built-in infrastructure, connected modules, and validated defaults reduce the need for repeated handoffs just to complete routine analysis.
That shortens the distance between generating data and learning from it. It also helps researchers stay closer to the scientific questions driving the work.
Meaningful Analysis Without Constant Supervision
iSCanGuide v3.0 helps non-specialist users do more than review static outputs. They can run meaningful single-cell and spatial workflows, inspect results in context, and move forward with less dependence on constant computational support.
A Tour of the Most Important v3.0 Enhancements
Several release highlights define the iSCanGuide v3.0 experience. Together, they make the platform feel more responsive, more unified, and better suited to modern large-scale research.
Redesigned UI for End-to-End Analysis
The redesigned interface helps researchers move from data intake through downstream interpretation in one place. Inputs from Xenium, Visium, CosMx, standard Cell Ranger pipelines, AnnData, and other supported formats can feed into a workflow that stays connected from QC through visualization and export.
AI-Powered Atlas-Level Annotation
Atlas-scale annotation can be one of the most time-intensive parts of large single-cell analysis. iSCanGuide v3.0 supports SingleR, CellTypist, and Geneformer so researchers can apply multiple annotation strategies in the same environment and compare outputs more efficiently.
Spatially Aware Trajectory Inference and Slingshot
iSCanGuide v3.0 expands trajectory analysis with options that fit different datasets. StaVia is the default choice for spatial data and large datasets, while Slingshot is available for smaller non-spatial embeddings and supports datasets up to 250,000 cells.
That flexibility helps researchers choose the right method without moving their work into a separate analytical environment.
Atlas-Scale Zoom and Exploration
Server-side zoom helps keep large datasets interactive, from whole tissue sections down to individual transcripts. For teams working with spatial data, that makes it easier to inspect biological patterns across multiple levels of detail without sacrificing responsiveness.
How iSCanGuide v3.0 Fits Advaita Bio’s Larger Goal
Advaita Bio builds tools that help researchers move from complex biological data to meaningful insight with more speed and confidence. iPathwayGuide already supports pathway-level interpretation for more than 13,000 researchers worldwide, and iSCanGuide extends that same push toward usable, rigorous upstream analysis.
That is what makes this release important. iSCanGuide v3.0 reflects a larger effort to make sophisticated science more efficient and more accessible, so researchers can spend less time managing analysis mechanics and more time advancing discovery.
Frequently Asked Questions About iSCanGuide v3.0
What kinds of data does iSCanGuide v3.0 support?
iSCanGuide supports inputs from Xenium, Visium, CosMx, standard Cell Ranger pipelines, AnnData files, and other supported formats used in single-cell and spatial workflows.
Who is iSCanGuide v3.0 built for?
iSCanGuide v3.0 is built for both experienced computational researchers and researchers who want to run meaningful analyses without deep computational expertise.
What is new about trajectory analysis in v3.0?
iSCanGuide v3.0 includes StaVia for spatial data and large datasets, along with Slingshot for smaller non-spatial datasets up to 250,000 cells.
How does iSCanGuide help with reproducibility?
iSCanGuide keeps analysis provenance connected to the outputs it generates, helping your team review methods, track decisions, and share results more confidently.
How does iSCanGuide connect to iPathwayGuide?
iSCanGuide includes a direct path to iPathwayGuide for pathway-level interpretation after differential expression analysis, helping researchers move from cell-level results to mechanistic insight with fewer extra steps.