Semantic Coherence: ariadne.ai – Signal Evidence & AI Readability

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[H1] Where Microscopy Meets Discovery

Solve the analysis bottleneck in your microscopy projects.
Access our AI image analysis solutions for spatial biology, volume electron microscopy, neuron tracing and more.

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[IMG: Where Microscopy Meets Discovery]

Trusted by more than 50 world-leading research labs.
>50 publications
>300 terabytes processed

Spatial Biology

Volume EM

Neuron Tracing

[H2] SPATIAL TM

Multiplex image analysis right here in your web browser.
World-class segmentation and registration. Neuroscience toolkit. For multi-channel Immunofluorescence, spatial proteomic, transcriptomics and more.

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[H2] 3dEMtrace

Reconstruct serial electron microscopy and tomography volumes. Reveal cellular structure in unprecedented detail. Map mitochondria, synapses, nuclei, ER and more.

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[H2] LMtraceTM

Neuron reconstruction made easy
LMtrace is our worry-free pipeline for reconstruction of neurons and glia cells in light microscopy datasets. Just upload your dataset, and we take care of the rest!

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[H2] applications

[H4] Comprehensive in silico tissue characterization in Alzheimer's and Parkinson's disease by spatial proteomics
Learn how ariadne.ai's cloud-based SPATIALTM platform helps discover spatial signatures that differentiate health from disease in CNS tissue. This application note walks you through neuron and glia segmentation at single-cell resolution from diverse markers (NeuN, IBA1, GFAP) and classification of pathological protein aggregates (including p-Tau, α-Synuclein, TDP-43 and Amyloid β).
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[H4] Webinar: High-plex immunohistochemistry - Spatial biology links patient survival with lymph node B cell responses in head & neck cancer
Dr. Ferdinando Pucci discusses his development of a high-plex immunohistochemistry (IHC) protocol and its applications in cancer biology. Learn how SPATIALTM corrects complex tissue deformations with its elastic registration workflow and allows researchers to discover spatial biomarkers subsequent to marker-based phenotyping.
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[H4] Scalable segmentation in volume electron microscopy (vEM)
Learn how to leverage ariadne.ai's 3dEMtrace(TM) service to scalably and reliably segment diverse structures from vEM, such as cells, synapses, endoplasmic reticulum, mitochondria, Golgi apparatus and much more.
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[H4] Webinar: Identification of microenvironment-dependent myeloid cell heterogeneity in AD with spatial biology
Dr. Bahareh Ajami discusses her research on myeloid cells in Alzheimer's disease using SPATIALTM, highlighting precise cell segmentation, subcellular proteomic analysis, and microenvironment-level insights into neuropathology.
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[H4] Webinar: Decoding Neurodegeneration

Dr. Birgitt Schuele discusses how high-plex spatial proteomics and spatial biology are advancing neuroscience discovery and translating spatial insights into breakthroughs in brain science.
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[H2] Meet Us

[H2] Selected Publications

More

Over the years our services and deep-learning techonology have been used for many high-profile
scientific publications. Below you find a collection of image analysis use cases or visit our News
site to learn more about recent publications and conference contributions.

[H5]
The role of the sodium-bicarbonate cotransporter Slc4a5 in retinal feedback mechanisms
Morikawa et al., Neuron 2024
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[H5]
Regulation of liver subcellular architecture controls metabolic homeostasis
Parlakgül et al., Nature 2022
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[H5]
Transverse endoplasmic reticulum expansion in hereditary spastic paraplegia corticospinal axons
Zhu et al., Human Molecular Genetics 2022
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[H5]
ESCRT-mediated membrane repair protects tumor-derived cells against T cell attack
Ritter et al., Science 2022
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[H5]
Whole-body integration of gene expression and single-cell morphology
Vergara et al., Cell 2021
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[H5]
Vasculogenesis in kidney organoids upon transplantation
Koning et al., npj Regenerative Medicine 2022
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[H2] What our clients say

[H3] Dr. Ferdinando Pucci

[H5] Assistant Professor, OHSU

[H5] Scientifically excellent
They supported our lab's immuno-oncology work from start to finish. We had some challenging data for them, and they tuned their registration and segmentation to handle it perfectly.

[H3] Dr. Oliver Braubach

[H5] Director of R&D, Canopy Biosciences

[H5] Great segmentation
Their neuron and glia segmentation is the best I've seen yet.

[H3] Dr. Bahareh Ajami

[H5] Assistant Professor, OHSU

[H5] Super responsive
The ariadne.ai team was always there to handle our custom requests quickly and with great scientific rigor. Their neuron and glia segmentation is fantastic.

[H3] Dr. C.Shan Xu

[H5] Professor of Cellular & Molecular Physiology, Yale School of Medicine

[H5] Beautiful segmentation
Ariadne.ai has repeatedly and consistently produced beautiful, top-notch segmentations on the 3D data we generated.

[H3] Dr. Anton Arkhipov

[H5] Investigator, Allen Institute

[H5] Great Experience
Everyone has been very helpful and it's been a great experience working with them. Ariadne has been a great partner in this project.

[H2] Latest News

Products

SPATIALTM
3dEMtrace
LMtraceTM

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[H1] Spatial biology image analysis here in your web browser.

World-class segmentation and registration. Neuroscience toolkit.
For multi-channel Immunofluorescence, spatial proteomic, transcriptomics and more.

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World-class cell segmentation.

Also for cells with complex morphologies such as neurons and glia. Supports CD45, NeuN, Iba1, GFAP, DAPI and many more.

Neuropathology analysis.

Classify pathological protein aggregates of Amyloid β, pTau, α-Synuclein, TDP43 and more.

Segment H&E images.

Leverage well-established IHC protocols, multiplexed.

Elastic registration.

Correct complex deformations across consecutive staining cycles, protocols or physical sections.

[H2]
Quantify complex cellular morphologies in detail

Detailed segmentation from fluorescent markers such as NeuN, IBA1, GFAP,
CD45 and more enables precise marker mapping and morphometric quantification.

[H2]
Correct complex image distortions

The elastic alignment workflow allows you to integrate different staining protocols (e.g., spatial proteomics and spatial transcriptomics) on the same section or across consecutive physical sections.

[H2]
Discover and count cell phenotypes by clustering

Leverage a flexible combination of manual gating, automated cell clustering, and marker-independent tissue segmentation to group cells into biologically meaningful phenotypes. Analyze and compare these clusters across conditions, regions, or tissue types to uncover spatial patterns and functional insights.

[H2]
Discover spatial biomarkers

Go beyond traditional single-cell analysis by identifying spatial biomarkers that capture the architecture and context of tissue. SPATIAL quantifies features such as cell shape, location, size and branching patterns — unlocking new classes of digital biomarkers that reflect molecular, morphological and spatial complexity.

[H2] Workflow

SPATIALTM provides access to an end-to-end image analysis workflow — from data upload to spatial biomarker discovery.

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[H2] applications

More

[H5]
Comprehensive in silico tissue characterization in Alzheimer's and Parkinson's disease by spatial proteomics
Learn more

[H5]
Webinar: High-plex immunohistochemistry - Spatial biology links patient survival with lymph node B cell responses in head & neck cancer
Learn more

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[H2] Start analyzing data
today

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[H2]
Frequently asked questions
Everything you need to know about the product and
billing.

[H2]
What file types can I upload?

Most common file types are supported, and we keep adding more. Currently supported file types include OME-TIFF, raw TIFF series, Zeiss CZI, Leica LIF and also include the datasets generated by Akoya Phenocycler, Bruker Spatial Biology CosMx and CellScape, Lunaphore COMET, 10xGenomics Visium, VisiumHD, Xenium and Vizgen MERSCOPE.

[H2]
What omics modalities are supported? What devices or protocols are supported?

SPATIALTM can integrate stacks of dense images (e.g., IHC or IF image series) and sparse images (e.g., lists of coordinates generated by mISH). This makes it broadly compatible with analysis workflows in spatial proteomics, transcriptomics and metabolomics. It's confirmed to work well with Akoya Phenocycler, Bruker Spatial Biology CosMx and CellScape, Lunaphore COMET, 10xGenomics Visium, VisiumHD, Xenium and Vizgen MERSCOPE and more.

[H2]
Can I run my own, custom analyses?

We provide comprehensive API access, allowing you to develop your own scripts to interface with SPATIALTM.

[H2]
What does it cost?

SPATIALTM is available through an affordable, simple and transparent pay-as-you-go model. We are happy to provide a custom quote for bulk orders or if you'd like to outsource the end-to-end analysis workflow to us.

[H2]
What are the hardware requirements?

SPATIAL works on any modern browser, leveraging cloud computing for processing. This means you can use our platform even on low-powered machines.

[H2]
How does your registration process work?

It's fully elastic, and scalable to arbitrary size. Some data can't be analyzed without this, but we've found that even nominally well-aligned data can profit from running our registration pipeline. Pixel-perfect precision is essential to get minimal cross-talk!

[H2]
How do you segment cells?

We segment cells using image channels that outline cellular morphology, optionally combined with a nucleus channel. The method works on any image channel on which cell outlines can be made out. For example, antibody-derived stains of CD45, NeuN, Iba1, GFAP, DAPI and many more can be used, but H&E or Hematoxylin staining works as well. Multiple markers can be combined for segmentation.

[H2]
What is the maximum dataset size?

There is no set limit on dataset size. 2-dimensional datasets are billed per dataset; 3-dimensional datasets are billed by amount of data.

[H2]
What payment options do you accept?

The fees are invoiced to institutions, payable via bank transfer.

[H2]
How are the results delivered?

Results are accessible through the SPATIAL browser interface and downloadable in standard formats through the user interface, or through an API for advanced users.

[H2]
Is my data safe with you?

We take data security very seriously. All data provided by our customers is kept strictly confidential and maintained on secure, EU-based and ISO 27001-compliant infrastructure.

[H2]
Where can I learn more?

For more information, schedule a personalized remote demo right here on this website! We're also happy to arrange an on-site visit if we're in your area.

[H2] Latest News

[H3] From entire cell to organelle segmentation
We can segment cell and cell structure of mitochondria, golgi apparatus, lysosomes, nuclear membranes, endoplasmic reticulum, lipid droplets, endosomes, all according to your specification.

[H3] New Cristae Segmentation
In addition to volume segmentation of mitochondria, we now also offer detailed reconstruction of cristae.

[H3] Secure Upload and Storage
All uploads are encrypted, and get securely stored and backed up on storage servers located in the EU.

[H3] Highest Scientific Standards
We commit ourselves to delivering high-quality results by combining latest machine-learning research with in-house proofreading by our QA team, all holding Master degrees in Biology.

My dataset contains multiple neurons, but I only want to trace a subset of them. What should I do?
When submitting a dataset, you can add a custom message to us. Please indicate which objects you want to have traced or to inform us about other relevant details.

What file types can I upload?
We currently accept TIFF and ZIP files. Please make sure to compress your dataset into a ZIP archive if it consists of multiple image files.

What is the maximum dataset size?
The maximum file size is 100 GiB. If your dataset exceeds this size, please get in touch with us, and we will prepare a custom quote for you.

What payment options do you accept?
You can pay with credit card (via stripe) or by wire transfer. For the latter, you will receive an invoice with your order details after you submit your dataset.

How are the results delivered?
Reconstructed neurons are provided in SWC format. If you require any other file format, please get in touch with us at contact@ariadne.ai.

How long do the reconstructions take?
Usually, your order will be reconstructed within 1–2 weeks. The duration will depend on the difficulty of the reconstruction task and the number of cells. You will be notified by e-mail once your results are ready for download.

Is my data safe with you?
We take data security very seriously. All data provided by our customers is kept strictly confidential and maintained on secure infrastructure.