AllenNeuralDynamics · arielleleon · Jun 26, 2026 · Jun 26, 2026 · Jun 26, 2026 · Jun 29, 2026
diff --git a/docs/source/aind/core_services.md b/docs/source/aind/core_services.md
@@ -1,6 +1,6 @@
 # Core Services
 
-The interactions between many of these services are illustrated in the [AIND software diagrams](./diagrams.md).
+The interactions between many of these services are illustrated in the [AIND software diagrams](../diagrams/index.md).
 
 **aind-data-transfer-service**
 

diff --git a/docs/source/aind/diagrams.md b/docs/source/aind/diagrams.md
diff --git a/docs/source/diagrams/data_acquisition.md b/docs/source/diagrams/data_acquisition.md
@@ -0,0 +1,13 @@
+# Data Acquisition
+
+:::{note}
+This diagram is a **proposal** for the instrumentation software architecture — a
+planned design rather than a system currently in production.
+:::
+
+This diagram presents a proposed software architecture for AIND instrumentation
+during data acquisition. It outlines how the acquisition software components are
+intended to interact to control the instrument and capture data during an
+experiment.
+
+![SIPE instrument diagram](mid_level/sipe_instrument.drawio.svg)
diff --git a/docs/source/diagrams/data_staging.md b/docs/source/diagrams/data_staging.md
@@ -0,0 +1,28 @@
+# Data Staging
+
+The local data center hosts a variety of services that stage and process data on
+its way to the cloud:
+
+`aind-data-transfer-service`
+: FastAPI service that accepts and validates data upload requests, retrieves the
+associated metadata, and dispatches compression and transfer jobs to the workflow
+manager for execution on the HPC cluster.
+
+`aind-airflow-service`
+: Apache Airflow–based workflow manager that schedules, submits, and monitors the
+data processing and upload jobs.
+
+`slurm`
+: HPC cluster for processing and upload tasks.
+
+`aind-metadata-service`
+: REST API that compiles and returns `aind-data-schema` metadata, aggregating and
+mapping records from multiple upstream data providers.
+
+`VAST`
+: Shared storage.
+
+Container registry
+: Docker images used to run processing jobs.
+
+![Local data center flow](mid_level/local_data_center_flow.drawio.svg)
diff --git a/docs/source/diagrams/data_storage_processing.md b/docs/source/diagrams/data_storage_processing.md
@@ -0,0 +1,35 @@
+# Data Storage and Processing
+
+## Code Ocean pipeline
+
+Raw data lands in S3 as a single data asset that carries its `aind-data-schema`
+metadata, with all of a session's modalities associated with one object.
+Processing pipelines are modality-specific — each pipeline processes a single
+modality. A pipeline outputs an NWB file along with `aind-data-schema` metadata,
+including processing metrics and quality control artifacts and metrics. Once the
+outputs have been QC'd, they can be combined into a final NWB file with its
+associated metadata.
+
+Each pipeline wraps modality- and platform-specific libraries that handle the
+underlying data processing, quality control, and NWB packaging.
+
+![Code Ocean pipeline diagram](mid_level/codeocean_pipeline_diagram.svg)
+
+
+
+## Quality control
+
+Each pipeline produces quality control artifacts and metrics alongside its
+processed outputs, captured in the asset's `aind-data-schema` metadata. These are
+surfaced through the [QC portal](https://github.com/AllenNeuralDynamics/aind-qc-portal),
+a web application for viewing and annotating quality control metadata for AIND
+data assets. The portal pulls QC metadata from the document database and displays
+the corresponding reference figures from the Code Ocean data assets.
+
+Reviewers use the portal to evaluate metrics marked `PENDING`, supporting AIND's
+two-step quality control process: first assessing whether an asset's data is
+suitable for analysis, then evaluating individual components (such as neurons)
+within the asset for usability.
+
+![QC diagram](mid_level/QC.drawio.svg)
+
diff --git a/docs/source/diagrams/dynamic_foraging.md b/docs/source/diagrams/dynamic_foraging.md
@@ -0,0 +1,40 @@
+# Dynamic foraging diagrams
+
+These diagrams outline the architecture of the Dynamic Foraging platform.
+
+## Lab Management System
+
+Dynamic Foraging relies on the lab management system for session and subject
+planning. It also uses the system's water restriction tracking to support
+behavior training.
+
+![Dynamic Foraging lab management](dynamic_foraging/mid_level/lab_management_df.svg)
+
+## Data Acquisition
+
+![Dynamic Foraging acquisition architecture](dynamic_foraging/dynamic_foraging_architecture.svg)
+
+## Data Storage and Processing
+
+### Mid-level Processing Pipeline
+
+Data from Dynamic Foraging is processed by two pipelines — a behavior pipeline
+and a fiber pipeline. Each runs independently and produces a modality-specific
+NWB file when it completes successfully.
+
+![Dynamic Foraging processing pipeline](dynamic_foraging/mid_level/codeocean_pipeline_diagram_DF.svg)
+
+#### Fiber Pipeline
+
+![Dynamic Foraging fiber pipeline](dynamic_foraging/mid_level/codeocean_pipeline_diagram_DF_fiber.svg)
+
+#### Behavior Pipeline
+
+![Dynamic Foraging behavior pipeline](dynamic_foraging/mid_level/codeocean_pipeline_diagram_DF_behavior.svg)
+
+### Low-level Processing Pipeline Library
+
+This pipeline processes raw Harp hardware signals into the trials table, packages
+the data into NWB, and runs QC on both the raw and processed data.
+
+![Dynamic Foraging low-level processing](dynamic_foraging/low_level/dynamic-foraging-low-level-processing.svg)