docs: more skeleton, adding processing page

Author: dbirman

docs/source/acquire_upload.md

@@ -16,4 +16,5 @@
 acquire_upload/prepare_before_acquisition
 acquire_upload/on_rig
 acquire_upload/upload
+acquire_upload/processing
 ```

docs/source/acquire_upload/on_rig.md

@@ -1,9 +1,13 @@
 # On rig
 
-During data acquisition you are responsible for running version-controlled acquisition software and ensuring your data files are organized according to a standardized system. Metadata generated during acquisition captures **what data** should appear in the final NWB files after processing, as well as **what manipulations** were performed (both behavioral stimuli and any procedures).
+During data acquisition you are responsible for running version-controlled acquisition software and ensuring your data files for each modality are organized according to standardized conventions.
 
-## Data file standards
+Metadata generated during acquisition captures **what data** should appear in the final NWB files after processing, as well as **what manipulations** were performed (both behavioral stimuli and any procedures).
+
+## Data organization conventions
 
 Raw data assets should be organized by modality.
 
-## 
+### Per-modality file standards
+
+## Acquisition metadata

docs/source/acquire_upload/processing.md

@@ -1,2 +1,39 @@
-# Per-modality pipelines
+# Processing pipelines
 
+Scientific computing is currently re-organizing pipelines to be per-modality, rather than per-project.
+
+## Per-modality physiology pipelines
+
+| Modality | Modalities | Pipeline repository |
+|---|---|---|
+| Barcoded anatomy resolved by sequencing | `barseq` | (no pipeline listed) |
+| Brightfield microscopy | `brightfield` | (no pipeline listed) |
+| Confocal microscopy | `confocal` | (no pipeline listed) |
+| Extracellular electrophysiology | `ecephys` | [aind-ephys-pipeline](https://github.com/AllenNeuralDynamics/aind-ephys-pipeline) |
+| Electron microscopy | `EM` | (no pipeline listed) |
+| Electromyography | `EMG` | (no pipeline listed) |
+| Fiber photometry | `fib` | [aind-fiber-photometry-harp-pipeline](https://github.com/AllenNeuralDynamics/aind-fiber-photometry-harp-pipeline) |
+| Fluorescence micro-optical sectioning tomography | `fMOST` | (no pipeline listed) |
+| Intracellular electrophysiology | `icephys` | (no pipeline listed) |
+| Intrinsic signal imaging | `ISI` | (no pipeline listed) |
+| Multiplexed analysis of projections by sequencing | `MAPseq` | (no pipeline listed) |
+| Multiplexed error-robust fluorescence in situ hybridization | `merfish` | (no pipeline listed) |
+| Magnetic resonance imaging | `MRI` | (no pipeline listed) |
+| Planar optical physiology | `pophys` | [aind-pophys-pipeline](https://github.com/AllenNeuralDynamics/aind-pophys-pipeline) |
+| Single cell RNA sequencing | `scRNAseq` | (no pipeline listed) |
+| Random access projection microscopy | `slap2` | (no pipeline listed) |
+| Selective plane illumination microscopy | `SPIM` | (no pipeline listed) |
+| Serial two-photon tomography | `STPT` | (no pipeline listed) |
+
+## Behavior pipelines
+
+| Modality | Modalities | Pipeline repository |
+|---|---|---|
+| Patch foraging behavior | `behavior`, `behavior-videos` | [aind-vr-foraging-pipeline](https://github.com/AllenNeuralDynamics/aind-vr-foraging-pipeline) |
+
+## Per-project pipelines
+
+| Modality | Modalities | Pipeline repository |
+|---|---|---|
+| Camstim/Sync Behavior | `behavior`, `behavior-videos`, `pophys`, `ephys` | [aind-behavior-camstim-pipeline](https://github.com/AllenNeuralDynamics/aind-behavior-camstim-pipeline) |
+| Dynamic foraging behavior| `behavior`, `behavior-videos`, `fib` | [aind-dynamic-foraging-pipeline](https://github.com/AllenNeuralDynamics/aind-dynamic-foraging-pipeline) |

docs/source/explore_analyze/analysis_framework.md

@@ -1,3 +1,3 @@
 # Analysis framework
 
-The [Analysis Framework](https://codeocean.allenneuraldynamics.org/capsule/3390834/tree/v1) is a Code Ocean pipeline that provides a template for facilitating large-scale analysis for data assets. Use the analysis framework anytime your analysis capsule(s) need to be run at scale on many individual data assets.
+The [Analysis Framework](https://github.com/AllenNeuralDynamics/aind-analysis-pipeline-template) is a Code Ocean pipeline that provides a template for facilitating large-scale analysis for data assets. Use the analysis framework anytime your analysis capsule(s) need to be run at scale on many individual data assets.

docs/source/explore_analyze/code_ocean.md

@@ -0,0 +1 @@
+# Ad-hoc analysis on Code Ocean

docs/source/explore_analyze/data_portal.md

@@ -0,0 +1 @@
+# Data portal

docs/source/explore_analyze/quality_control.md

@@ -0,0 +1 @@
+# Quality control