Proscia

Proscia Concentriq® Embeddings extracts H-Optimus embeddings from slides in a Concentriq® LS workspace — no downloading, tiling, or self-hosted server required. It’s the best fit when your slides already live in Concentriq® LS: Proscia tiles each slide, runs the model, and returns one safetensor file of embeddings per slide.

This integration is operated by Proscia. Bioptimus provides the H-Optimus foundation model; Proscia provides the Concentriq® platform, the embeddings service, and the proscia-ai-tools client. For platform access, workspace provisioning, and support, contact Proscia.

How it works

Slides live in Concentriq® LS

Your whole-slide images are stored in your Concentriq® LS workspace. Nothing is downloaded locally.

Select H-Optimus and request embeddings

Using the proscia-ai-tools Python client, you point at one or more image repositories, pick the H-Optimus model tag, and submit an embedding job. The call returns a ticket ID.

Proscia runs inference

Concentriq® Embeddings tiles each slide at your chosen magnification and runs H-Optimus on Proscia’s infrastructure.

Pull embeddings back

Fetch the results by ticket ID. Each slide comes back as a compact safetensor file of feature vectors that you load into memory for downstream tasks.

1. Install the client

Install the client directly from GitHub:

pip install git+https://github.com/Proscia/proscia-ai-tools.git

2. Authenticate

The client connects to your Concentriq® workspace endpoint. It supports three authentication methods — provide exactly one:

from proscia_ai_tools.client import ClientWrapper as Client

client = Client(
    url="https://<your-workspace>.concentriq.proscia.com",
    email="<your-email>",
    password="<your-password>",
)

from proscia_ai_tools.client import ClientWrapper as Client

client = Client(
    url="https://<your-workspace>.concentriq.proscia.com",
    api_key="<your-concentriq-api-key>",
)

from proscia_ai_tools.client import ClientWrapper as Client

client = Client(
    url="https://<your-workspace>.concentriq.proscia.com",
    token="<your-jwt-token>",
)

Your workspace URL and credentials are issued by Proscia. Keep them out of source control — load them from environment variables or a secrets manager rather than hard-coding them.

3. Generate embeddings with H-Optimus

Submit an embedding job against one or more Concentriq® image repositories, selecting the H-Optimus model tag and the microns-per-pixel (mpp) resolution. The call returns a ticket ID for retrieving the results.

# Submit an embedding job for one or more repositories.
ticket_id = client.embed_repos(
    ids=[1234],                      # Concentriq® repository IDs
    model="bioptimus/H-optimus-1",   # H-Optimus foundation model tag
    mpp=0.5,                           # target resolution (microns per pixel)
)

# Retrieve the embeddings once the job completes.
embeddings = client.get_embeddings(ticket_id)

The client also exposes embed_images (for specific image IDs) and embed_roi (for annotation- or region-based embeddings). See the proscia-ai-tools client for the full API.

The model tag selects the foundation model Concentriq® Embeddings runs. Use the H-Optimus tag published by Proscia for your workspace; the exact set of available models is controlled by Proscia and may expand over time.

4. Explore end-to-end examples

Proscia maintains runnable notebooks for complete workflows — embedding generation, regions of interest, annotations, clustering, segmentation, and zero-shot classification:

Proscia example notebooks

Browse the notebooks/ folder in proscia-ai-tools for end-to-end Concentriq® Embeddings workflows using H-Optimus.

When to use a different option

Slides not in Concentriq®?

If your slides live outside Concentriq® LS, deploy H-Optimus or M-Optimus via AWS, on-premise, or Hugging Face.

Need whole-slide tooling?

The Bioptimus SDK handles tiling, tissue masking, and output formats against a Bioptimus-deployed server.

Get Started

Platforms

How it works

1. Install the client

2. Authenticate

3. Generate embeddings with H-Optimus

4. Explore end-to-end examples

Proscia example notebooks

When to use a different option

Slides not in Concentriq®?

Need whole-slide tooling?

​How it works

​1. Install the client

​2. Authenticate

​3. Generate embeddings with H-Optimus

​4. Explore end-to-end examples

Proscia example notebooks

​When to use a different option

Slides not in Concentriq®?

Need whole-slide tooling?

How it works

1. Install the client

2. Authenticate

3. Generate embeddings with H-Optimus

4. Explore end-to-end examples

When to use a different option