Get started with Console

Console is the web interface of the Aignostics Platform. This guide takes you through your first analysis with Atlas H&E-TME, which profiles the tumor microenvironment on H&E slides: you upload your slides with one command, then start the analysis and download the results in your browser. It takes about 15 minutes plus upload time, and you don’t need to know how to code.

You need a Mac, Windows, or Linux computer, a phone for the login code, and your slides as .svs, .tif, .tiff, or DICOM .dcm files.

Sign up for the Aignostics Platform

You need an account on the Aignostics Platform. If you already have one, skip this section.

  1. Find your invitation email from support@aignostics.com, with the subject “You’ve been invited to join your organization’s Aignostics account”.

  2. Accept the invitation in the email, then enter your full name and set a password.

  3. Set up two-factor authentication: install Google Authenticator (Android, iPhone) or a similar app, scan the code shown in your browser, and enter the six-digit code the app gives you.

Upload your slides

1. Install the Aignostics Python SDK

  1. Open a terminal. On macOS, press Cmd+Space, type Terminal, and press Enter. On Windows, open the Start menu, type PowerShell, and press Enter.

  2. Paste the install command for your system into the terminal and press Enter:

    # macOS or Linux
curl -LsSf https://astral.sh/uv/install.sh | sh

    # Windows
powershell -ExecutionPolicy ByPass -c "irm https://astral.sh/uv/install.ps1 | iex"

  3. Close the terminal and open a new one.

  4. Check the install by running in your terminal:

    uvx aignostics --help

    You should see a list of commands.

2. Log in

  1. Log in by running in your terminal:

    uvx aignostics user login

  2. In the browser window that opens, log in with your email, password, and the six-digit code from your authenticator app.

You stay logged in for future sessions.

3. Upload your slides from your local disk

  1. Put the slides you want to upload in one folder on your local disk.

  2. Upload the folder by running the following, replacing ./my-slides with its path:

    uvx aignostics bucket upload ./my-slides

  3. Keep the terminal open until it prints All files uploaded successfully!. Slides are large, so this can take a while.

Your slides are now in the bucket Aignostics provides for your organization, in a folder named after your computer’s user account, for example jdoe.

4. (Optional) Copy slides from your own cloud bucket

If your slides are already stored in AWS S3, Azure Blob Storage, or Google Cloud Storage, you can copy them directly from there into your Aignostics bucket.

  1. Install rclone, a tool for managing cloud storage, by following the rclone installation guide.

  2. Log in to your own cloud provider account (aws sso login, az login, or gcloud auth application-default login).

  3. Log in to your Aignostics account if you haven’t already and get the access keys for your Aignostics bucket by running:

    uvx aignostics user whoami --no-mask-secrets

    Note aignostics_bucket_name, aignostics_bucket_hmac_access_key_id, and aignostics_bucket_hmac_secret_access_key — these are your access credentials. Treat them like a password.

  4. Use the access credentials from the previous step to register both your own cloud bucket and your Aignostics bucket with rclone by running:

    rclone config create aignx s3 provider=GCS endpoint=https://storage.googleapis.com \
  access_key_id=<access key id> secret_access_key=<secret> no_check_bucket=true

# and one of these, depending on your cloud:
rclone config create mycloud s3 provider=AWS env_auth=true region=<your-region>
rclone config create mycloud azureblob env_auth=true account=<your-storage-account>
rclone config create mycloud "google cloud storage" env_auth=true

  5. Copy your slides from your own bucket into a folder in your Aignostics bucket (for example, jdoe), by running:

    rclone copy mycloud:<your-bucket>/<slides-folder> aignx:<aignostics-bucket>/jdoe/ --progress

    Keep the process running and your machine awake until the copy finishes.

Analyze your slides with Atlas H&E-TME

5. Start the analysis

  1. Open platform.aignostics.com and select Analyze → My Application Runs in the sidebar.

  2. Click Create run in the top right.

  3. Under Slides, open your folder (Bucket » jdoe) and tick the slides to analyze.

    The Create run form with the bucket contents listed and one slide ticked

    Pick your slides from the bucket. Click to view full size.

  4. Under Version, pick the he-tme entry with the highest version number.

  5. Under Indication and Tissue, pick what matches your slides, for example Lung cancer and Lung. They apply to all slides you selected.

  6. Under Name, enter anything that helps you recognize the analysis later.

    The lower half of the Create run form with Version, Staining method, Indication, Tissue and Name filled in

    The rest of the form, filled in for a lung slide. Click to view full size.

  7. Click Run now.

Your analysis appears at the top of My Application Runs.

6. Wait for results

The analysis runs on Aignostics servers, so you can close your browser. It takes anywhere from minutes to hours depending on the number and size of your slides. The Status column on My Application Runs shows Completed when it is done.

7. Review your results in the viewer

  1. Open your analysis and click a slide name to open it in the viewer.

  2. Use the Overlays panel on the right to show the tissue regions, classified cells, and quality-control flags on top of your slide.

A slide in the viewer with tissue and cell overlays switched on and the Overlays panel open

The viewer with tissue and cell overlays on. Click to view full size.

8. Download your results

On Run Details, click Download Available Results. For each slide you get the tissue regions, the classified cells, and a spreadsheet of measurements such as cell counts and densities. Results are kept for 30 days, so download what you want to keep.

The Run Details page with the Download Available Results button and per-slide download icons

Run Details — download everything at once, or one slide at a time. Click to view full size.

That’s it: you have analyzed your first slides with Atlas H&E-TME and have the results on your computer.

Where to go next

  • Invite your team — add colleagues so they can run analyses too.

  • Clean up your bucket — your slides stay in your bucket until you delete them, so analyzing them again needs no new upload. Deletion cannot be undone but does not affect results you have downloaded. It is a dry run by default; replace jdoe with the folder your slides are in:

    uvx aignostics bucket delete "jdoe/.*"              # shows what would be deleted
uvx aignostics bucket delete "jdoe/.*" --no-dry-run # deletes it