Please look at the notebooks in the `example` folder for a more detailed example
and read the
[client reference documentation](https://aignostics.readthedocs.io/en/latest/lib_reference.html)
to learn about all classes and methods.

##### Defining the input for an application run

Next to the `application_version` of the application you want to run, you have
to define the input items you want to process in the run. The input items are
defined as follows:

For each item you want to process, you need to provide a unique `reference`
string. This is used to identify the item in the results later on. The
`input_artifacts` field is a list of `InputArtifact` objects, which defines what
data & metadata you need to provide for each item. The required artifacts depend
on the application version you want to run - in the case of test application,
there is only one artifact required, which is the image to process on. The
artifact name is defined as `user_slide`.

The `download_url` is a signed URL that allows the Aignostics Platform to
download the image data later during processing.

#### Self-signed URLs for large files

To make the whole slide images you want to process available to the Aignostics Platform, you
need to provide a signed URL that allows the platform to download the data.
Self-signed URLs for files in google storage buckets can be generated using the
`generate_signed_url`
([code](https://github.com/aignostics/python-sdk/blob/407e74f7ae89289b70efd86cbda59ec7414050d5/src/aignostics/client/utils.py#L85)).

**We expect that you provide the
[required credentials](https://cloud.google.com/docs/authentication/application-default-credentials)
for the Google Storage Bucket**

## Platform

### Overview

The **Aignostics Platform** is a comprehensive cloud-based service that allows organizations to leverage advanced computational pathology applications without the need for specialized expertise or complex infrastructure. Via its API it provides a standardized, secure interface for accessing Aignostics' portfolio of advanced computational pathology applications. These applications perform machine learning based tissue and cell analysis on histopathology slides, delivering quantitative measurements, visual representations, and detailed statistical data.


### Key Features
Aignostics Platform offers key features designed to maximize value for its users:

1. **Run Aignostics applications:** Run Aignostics advanced computational pathology applications like [Atlas H&E-TME](https://www.aignostics.com/products/he-tme-profiling-product) on your whole slide images (WSIs) and receive results in a easy to inspect formats.
2. **Multiple Access Points:** Interact with the platform via various pathways, from **Aignostics Launchpad** (desktop application for MacOS, Windows and Linux), **Aignostics CLI** (command-line interface for your terminal or shell scripts), **Example Notebooks** (we support Jupyter and Marimo), **Aignostics Client Library** (for integration with your Python codebase), or directly through the **API of the Aignostics Platform** (for integration with any programming language). Contact your business partner at Aignostics if you are interested to discuss a direct integration with your Imaging Management Systems (IMS) and Laboratory Information Management Systems (LIMS).
3. **Secure Data Handling:** Maintain control of your slide data through secure self-signed URLs. Results are automatically deleted after 30 days, and can be deleted earlier by the user.
4. **High-throughput processing with incremental results delivery:** Submit up to 500 whole slide images (WSI) in one batch request. Access results for individual slides as they completed processing, without having to wait for the entire batch to finish.
5. **Standard formats:** Support for commonly used image formats in digital pathology such as pyramidal DICOM, TIFF, and SVS. Results provided in standard formats like QuPath GeoJSON (polygons), TIFF (heatmaps) and CSV (measurements and statistics).

### Registration and User Access

To start using the Aignostics Platform and its advanced applications, your organization must be registered by our business support team:

1. Access to the Aignostics Platform requires a formal business agreement. Once an agreement is in place between your organization and Aignostics, we proceed with your organization's registration. If your organization does not yet have an account, please contact your account manager or email us at [support@aignostics.com](mailto:support@aignostics.com) to express your interest.
2. To register your organization, we require the name and email address of at least one employee, who will be assigned the Administrator role for your organisation. Your organisation's Administrator can invite and manage additional users.

> [!Important]
> 1. All user accounts must be associated with your organization's official domain. We do not support the registration of private or personal email addresses.
> 2. For security, Two-Factor Authentication (2FA) is mandatory for all user accounts.
> 3. We can integrate with your IDP system (e.g. SAML, OIDC) for user authentication. Please contact us to discuss the integration.
> 4. Registering your organistation typically takes 2 business days depending on the complexity of the signed business agreement and specific requirements.

### Console

The web-based [*Aignostics Console*](https://platform.aignostics.com) is a user-friendly interface that allows you to
manage your organization, applications, quotas, and users registered with the Aignostics Platform.

1. The Console is available to users registered for your organisation to manage their profile and monitor usage of their quota.
2. Administrators of your organization can invite additional users, manage the organisation and user specific quotas and monitor usage.
3. Both roles can trigger application runs.

### Applications
An application is a fully automated advanced machine learning based workflow composed of one or more specific tasks (e.g. Tissue Quality Control, Tissue Segmentation, Cell Detection, Cell Classification and predictive analysis). Each application is designed for a particular analysis purpose (e.g. Tumor Micro Environment analysis or biomarker scoring). For each application we define input requirements, processing tasks and output formats.

As contracted in your business agreement with Aignostics your organisation subscribes to one or more applications. The applications are available for your organization in the Aignostics Platform. You can find the list of available applications in the Console of the Aignostics Platform.

Each application can have multiple versions. Please make sure you read dedicated application documentation to understand its specific constraints regarding acceptable formats, staining method, tissue types and diseases.

Once registered to the Platform, your organization will automatically gain access to the "Test Application". This application can be used to configure the workflow and to make sure that the integration works correctly.

### Application run

To trigger the application run, users can use the Aignostics Launchpad, Aignostics CLI, Example Notebooks, our Client Library, or directly call the REST API. The platform expects the user payload, containing the metadata and the signed URLs to the whole slide images (WSIs). The detailed requirements of the payload depend on the application and are described in the documentation, and accessible via the Info button in the Launchpad, as well as via the CLI and `/v1/applications` endpoint in the API.

When the application run is created, it can be in one of the following states:

1. **received**: the application run received from the client
2. **scheduled**: the application run request is valid and is scheduled for execution
3. **running**: the application run execution started
4. **completed**: the application run execution is done and all outputs are available for download
5. **completed**: the application run execution is done, but some items end up in the failed state
6. **rejected**: the application run request is rejected before it is scheduled
7. **cancelled by the system**: the application run failed during the execution with the number of errors higher than the threshold
9. **cancelled by the user**: the application run is cancelled by the user before it is finished

The status and operations of an application run are private to the user who triggered the run.

### Results
When the processing of whole slide image is successfully completed, the resulting outputs become available for download. To assess specifics of application outputs please consult our application specific documentation, which you can find in the **Console**. Please note that you access to documentation is restricted to those applications your organisation subscribed to.

Application run outputs are automatically deleted 30 days after the application run has completed. However, the owner of the application run (the user who initiated it) can use the API to manually delete outputs earlier, once the run has reached a final state - completed, cancelled by the system or cancelled by the user. The Launchpad and CLI provide enable to delete results with one click resp. command.

### Quotas
Every organization has a limit on how many WSIs it can process in a calendar month. The following quotas exist:

1. **Per organization**: as defined in your business agreement with Aignostics
2. **Per user**: defined by your organization Admin

When the per month quota is reached, an application run request is denied.

Other limitations may apply to your organization:

1. Allowed number of users an organization can register
2. Allowed number of images user can submit per application run
3. Allowed number of parallel application runs for the whole organization

Additionally, we allow organization Admin to define following limitations for its users:

1. Maximum number of images the user can process per calendar month.
2. Maximum number of parallel application runs for a given user

Visit the [Console](https://platform.aignostics.com) to check your current quota and usage. The Console provides a clear overview of the number of images processed by your organization and by each user, as well as the remaining quota for the current month.

### API

The **Aignostics Platform API** is a RESTful web service that allows you to interact with the platform programmatically. It provides endpoints for submitting whole slide images (WSIs) for analysis, checking the status of application runs, and retrieving results.

You can interact with the API using the Python client, which is a wrapper around the RESTful API. The Python client simplifies the process of making requests to the API and handling responses. It also provides convenient methods for uploading WSIs, checking application run status, and downloading results.

For integration with programming languages other than Python, you can use the RESTful API directly. The API is designed to be language-agnostic, meaning you can use any programming language that supports HTTP requests to interact with it. This includes languages like Java, Kotlin, C#, Ruby, and Typescript.

### Cost

Every WSI processed by the Platform generates a cost. Usage of the "Test Application" is free of charge for any registered user. The cost for other applications is defined in your business agreement with Aignostics. The cost is calculated based on the number of slides processed. When an application run is cancelled, either by the system or by the user, only processed images incur a cost.

**[Read the API reference documentation](https://aignostics.readthedocs.io/en/latest/api_reference_v1.html)** or use our **[Interactive API Explorer](https://platform.aignostics.com/explore-api)** to dive into details of all operations and parameters.

## Further Reading

1. Inspect our
[security policy](https://aignostics.readthedocs.io/en/latest/security.html)
with detailed documentation of checks, tools and principles.
1. Inspect how we achieve
[operational excellence](https://aignostics.readthedocs.io/en/latest/operational_excellence.html)
with information on our modern toolchain and software architecture.
2. Check out the
[CLI reference](https://aignostics.readthedocs.io/en/latest/cli_reference.html)
with detailed documentation of all CLI commands and options.
3. Check out the
[library reference](https://aignostics.readthedocs.io/en/latest/lib_reference.html)
with detailed documentation of public classes and functions.
4. Check out the
[API reference](https://aignostics.readthedocs.io/en/latest/api_reference_v1.html)
with detailed documentation of all API operations and parameters. See as well
the OpenAPI Specification in [JSON](https://github.com/aignostics/python-sdk/blob/main/docs/source/_static/openapi_v1.json) and [YAML](https://github.com/aignostics/python-sdk/blob/main/docs/source/_static/openapi_v1.yaml), and the [API Explorer](https://aignostics.readthedocs.io/en/latest/api_explorer_v1.html).
5. Our
[release notes](https://aignostics.readthedocs.io/en/latest/release-notes.html)
provide a complete log of recent improvements and changes.
6. We gratefully acknowledge the numerous
[open source projects](https://aignostics.readthedocs.io/en/latest/attributions.html)
that this project builds upon. Thank you to all these wonderful contributors!

## Glossary

### A

**Administrator Role**
A user role within an organization that has permissions to invite and manage additional users, define user-specific quotas, and monitor organizational usage.

**Aignostics CLI**
Command-Line Interface that allows interaction with the Aignostics Platform directly from terminal or shell scripts, enabling dataset management and application runs.

**Aignostics Client Library**
Python library for seamless integration of the Aignostics Platform with enterprise image management systems and scientific workflows.

**Aignostics Console**
Web-based user interface for managing organizations, applications, quotas, users, and monitoring platform usage.

**Aignostics Launchpad**
Graphical desktop application (available for Mac OS X, Windows, and Linux) that allows users to run computational pathology applications on whole slide images and inspect results with QuPath and Python Notebooks.

**Aignostics Platform**
Comprehensive cloud-based service providing standardized, secure interface for accessing advanced computational pathology applications without requiring specialized expertise or complex infrastructure.

**Aignostics Platform API**
RESTful web service that allows programmatic interaction with the Aignostics Platform, providing endpoints for submitting WSIs, checking application run status, and retrieving results.

**Aignostics Python SDK**
Software Development Kit providing multiple pathways to interact with the Aignostics Platform, including the Launchpad, CLI, Client Library, and example notebooks.

**Application**
Fully automated advanced machine learning workflow composed of specific tasks (e.g., Tissue Quality Control, Tissue Segmentation, Cell Detection, Cell Classification) designed for particular analysis purposes.

**Application Run**
The execution instance of an application on submitted whole slide images, which can be in various states: received, scheduled, running, completed, rejected, cancelled by system, or cancelled by user.

**Application Version**
Specific version of an application with defined input requirements, processing tasks, and output formats. Each application can have multiple versions.

**Atlas H&E-TME**
Advanced computational pathology application for Hematoxylin and Eosin-stained Tumor Microenvironment analysis.

### B

**Base MPP (Microns Per Pixel)**
Metadata parameter specifying the resolution of whole slide images, indicating the physical distance represented by each pixel.

**Business Agreement**
Formal contract between an organization and Aignostics required for platform access, defining quotas, applications, and terms of service.

### C

**Checksum CRC32C**
Cyclic Redundancy Check used to verify data integrity of uploaded whole slide images.

**Client**
The main class in the Aignostics Python SDK used to initialize connections and interact with the platform API.

**Computational Pathology**
Field combining digital pathology with artificial intelligence and machine learning to analyze histopathology slides quantitatively.

**Aignostics Console**
Web-based user interface for managing organizations, applications, quotas, users, and monitoring platform usage.

### D

**DICOM (Digital Imaging and Communications in Medicine)**
Standard format for medical imaging data, supported by the Aignostics Platform for whole slide images.

**Download URL**
Signed URL that allows the Aignostics Platform to securely download image data during processing.

### G

**GeoJSON**
Standard format used by QuPath for representing polygonal annotations and results.

**Google Storage Bucket**
Cloud storage service where users can store whole slide images and generate signed URLs for platform access.

### H

**H&E (Hematoxylin and Eosin)**
Common histological staining method for tissue visualization, used in Atlas H&E-TME application.

**Heatmaps**
Visual representations of analysis results provided in TIFF format showing spatial distribution of measurements.

### I

**IDC (NCI Image Data Commons)**
Public repository of medical imaging data that can be queried and downloaded through the Aignostics CLI.

**IMS (Imaging Management Systems)**
Enterprise systems for managing medical imaging data that can be integrated with the Aignostics Platform.

**Input Artifact**
Data object required for application processing, including the actual data file and associated metadata.

**Input Item**
Individual unit of processing in an application run, containing one or more input artifacts with a unique reference identifier.

**Interactive API Explorer**
Tool for exploring and testing API endpoints and parameters interactively.

### J

**Jupyter**
Popular notebook environment supported by the Aignostics Platform for interactive analysis and visualization.

### L

**LIMS (Laboratory Information Management Systems)**
Laboratory systems that can be integrated with the Aignostics Platform for workflow automation.

### M

**Marimo**
Modern notebook environment supported by the Aignostics Platform as an alternative to Jupyter.

**Metadata**
Descriptive information about whole slide images including dimensions, resolution, tissue type, and disease information required for processing.

**MPP (Microns Per Pixel)**
See Base MPP.

### N

**NCI Image Data Commons (IDC)**
See IDC.

### O

**Operational Excellence**
Aignostics' commitment to high-quality software development practices including A-grade code quality, security scanning, and comprehensive documentation.

### P

**Pyramidal**
Multi-resolution image format that stores the same image at different zoom levels for efficient viewing and processing.

**Python SDK**
Software Development Kit providing multiple pathways to interact with the Aignostics Platform through Python programming language.

### Q

**QuPath**
Open-source software for bioimage analysis that can be launched directly from the Aignostics Launchpad to view results.

**Quota**
Limit on the number of whole slide images an organization or user can process per calendar month, as defined in business agreements.

### R

**Reference**
Unique identifier string for each input item in an application run, used to match results with original inputs.

**Results**
Output data from application processing, including measurements, statistics, heatmaps, and annotations, automatically deleted after 30 days.

**RESTful API**
Architectural style for web services that the Aignostics Platform API follows, enabling language-agnostic integration.

### S

**Self-signed URLs**
Secure URLs with embedded authentication that allow the platform to access user data without exposing credentials.

**SVS**
Aperio ScanScope Virtual Slide format, commonly used for whole slide images and supported by the platform.

### T

**Test Application**
Free application automatically available to all registered organizations for workflow configuration and integration testing.

**TIFF (Tagged Image File Format)**
Standard image format supported for both input whole slide images and output heatmaps.

**Tissue Segmentation**
Computational process of identifying and delineating different tissue regions within histopathology slides.

**TME (Tumor Microenvironment)**
The cellular environment surrounding tumor cells, analyzed by the Atlas H&E-TME application.

**Two-Factor Authentication (2FA)**
Mandatory security requirement for all user accounts on the Aignostics Platform.

### U

**UV**
Modern Python package manager used for dependency management and project setup in the SDK documentation.

**UVX**
Tool for running Python applications directly without explicit installation, used to execute Aignostics CLI commands.

### W

**Whole Slide Image (WSI)**
High-resolution digital image of an entire histopathology slide, the primary input format for computational pathology applications.