From f9c18ace982a807b22a628741c66e11e86448133 Mon Sep 17 00:00:00 2001 From: Arielle Leon Date: Thu, 4 Jun 2026 16:57:10 -0700 Subject: [PATCH 01/12] feat: add new pipeline processing diagrams --- .../codeocean_pipeline_diagram.drawio | 311 +++++++++++++----- .../mid_level/codeocean_pipeline_diagram.svg | 2 +- 2 files changed, 228 insertions(+), 85 deletions(-) diff --git a/docs/source/diagrams/mid_level/codeocean_pipeline_diagram.drawio b/docs/source/diagrams/mid_level/codeocean_pipeline_diagram.drawio index 2661df2..21131d3 100644 --- a/docs/source/diagrams/mid_level/codeocean_pipeline_diagram.drawio +++ b/docs/source/diagrams/mid_level/codeocean_pipeline_diagram.drawio @@ -1,131 +1,274 @@ - + - + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - - - + + + + + + + + + + + + + + + + + + + + + + - - - - + + + + + + + + - - - - + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + - - + + + + + + + + + + + + - - + + + + + + + + + + - - + + - - + + - - + + - - + + - - + + - - + + + + + + + + + - - + + - - + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + + + + + + + + + + + + + + + + + + + + + + + + + + + + - - + + - - + + - - + + - - + + diff --git a/docs/source/diagrams/mid_level/codeocean_pipeline_diagram.svg b/docs/source/diagrams/mid_level/codeocean_pipeline_diagram.svg index 357c6e8..218b5b9 100644 --- a/docs/source/diagrams/mid_level/codeocean_pipeline_diagram.svg +++ b/docs/source/diagrams/mid_level/codeocean_pipeline_diagram.svg @@ -1,4 +1,4 @@ -
Modality A
Modality A
Modality B
Modality B
Modality B
Modality B
Processing pipeline Flow
Processing pipeline Flow
Storage Layer
Storage Layer
S3
S3
DocDB
DocDB
Legend
Legend
Modality data
Modality data
Raw metadata
Raw metadata
Derived metadata
Derived metadata
Raw data asset
Raw data asset
Derived data asset
Derived data assetText is not SVG - cannot display \ No newline at end of file +
ppeline modality 1
DocDB
S3: aind-open-data
pipeline modality 2
pipeline modality 3
NWB File
a/ND schematized metadata
a/ND schematized metadata includes :
  • procedures.json
  • subject.json
  • data_description.json
  • processing.json
  • data_description.json
  • acquisition.json
  • instrument.json
a/ND schematized metadata
Raw Data
DocDB
S3: aind-open-data
DocDB
S3: aind-open-data
a/ND schematized metadata
Raw Data
Extract, process and package data
QC data in NWB file
quality_control.json
Plots
NWB File
processing.json
processing.json
quality_control.json
data_description.json
NWB File with a/ND Schematized Metadata
Aggregate QC
Aggregate processing
Package schematized metadata into NWB file
Plots and metrics
NWB File
a/ND schematized metadata
Plots and metrics
DocDB
S3: aind-open-data
NWB File
a/ND schematized metadata
Plots and metrics
NWB File
a/ND schematized metadata
Plots and metrics
NWB File
a/ND schematized metadata
Plots and metrics
Raw data come with one or more modalities
Raw data processed per modality
Modality based derived assets combined after processing is complete
 \ No newline at end of file From f74ecf6d75302c948b3b2651901a3f9e88db6249 Mon Sep 17 00:00:00 2001 From: Arielle Leon Date: Thu, 4 Jun 2026 16:59:51 -0700 Subject: [PATCH 02/12] fix: add titles and adjust layout --- .../codeocean_pipeline_diagram.drawio | 123 ++++++++++-------- .../mid_level/codeocean_pipeline_diagram.svg | 2 +- 2 files changed, 70 insertions(+), 55 deletions(-) diff --git a/docs/source/diagrams/mid_level/codeocean_pipeline_diagram.drawio b/docs/source/diagrams/mid_level/codeocean_pipeline_diagram.drawio index 21131d3..fff75d0 100644 --- a/docs/source/diagrams/mid_level/codeocean_pipeline_diagram.drawio +++ b/docs/source/diagrams/mid_level/codeocean_pipeline_diagram.drawio @@ -1,13 +1,13 @@ - + - + - + @@ -16,7 +16,7 @@ - + @@ -38,138 +38,138 @@ - + - + - + - + - + - + - + - - + + - + - - + + - + - + - + - + - + - + - + - + - + - + - - + + - - + + - + - - + + - - + + - - + + - - + + - + - + - + - + - - + + - - + + - + - - + + @@ -205,10 +205,10 @@ - + - + @@ -235,7 +235,7 @@ - + @@ -268,7 +268,22 @@ - + + + + + + + + + + + + + + + + diff --git a/docs/source/diagrams/mid_level/codeocean_pipeline_diagram.svg b/docs/source/diagrams/mid_level/codeocean_pipeline_diagram.svg index 218b5b9..d4977f3 100644 --- a/docs/source/diagrams/mid_level/codeocean_pipeline_diagram.svg +++ b/docs/source/diagrams/mid_level/codeocean_pipeline_diagram.svg @@ -1,4 +1,4 @@ -
ppeline modality 1
DocDB
S3: aind-open-data
pipeline modality 2
pipeline modality 3
NWB File
a/ND schematized metadata
a/ND schematized metadata includes :
  • procedures.json
  • subject.json
  • data_description.json
  • processing.json
  • data_description.json
  • acquisition.json
  • instrument.json
a/ND schematized metadata
Raw Data
DocDB
S3: aind-open-data
DocDB
S3: aind-open-data
a/ND schematized metadata
Raw Data
Extract, process and package data
QC data in NWB file
quality_control.json
Plots
NWB File
processing.json
processing.json
quality_control.json
data_description.json
NWB File with a/ND Schematized Metadata
Aggregate QC
Aggregate processing
Package schematized metadata into NWB file
Plots and metrics
NWB File
a/ND schematized metadata
Plots and metrics
DocDB
S3: aind-open-data
NWB File
a/ND schematized metadata
Plots and metrics
NWB File
a/ND schematized metadata
Plots and metrics
NWB File
a/ND schematized metadata
Plots and metrics
Raw data come with one or more modalities
Raw data processed per modality
Modality based derived assets combined after processing is complete
 \ No newline at end of file +
Pipeline Modality 1
DocDB
S3: aind-open-data
Pipeline Modality 2
pipeline modality 3
NWB File
a/ND schematized metadata
a/ND schematized metadata includes :
  • procedures.json
  • subject.json
  • data_description.json
  • processing.json
  • data_description.json
  • acquisition.json
  • instrument.json
a/ND schematized metadata
Raw Data
DocDB
S3: aind-open-data
DocDB
S3: aind-open-data
a/ND schematized metadata
Raw Data
Extract, process and package data
QC data in NWB file
quality_control.json
Plots
NWB File
processing.json
processing.json
quality_control.json
data_description.json
NWB File with a/ND Schematized Metadata
Aggregate QC
Aggregate processing
Package schematized metadata into NWB file
Plots and metrics
NWB File
a/ND schematized metadata
Plots and metrics
DocDB
S3: aind-open-data
NWB File
a/ND schematized metadata
Plots and metrics
NWB File
a/ND schematized metadata
Plots and metrics
NWB File
a/ND schematized metadata
Plots and metrics
Raw data come with one or more modalities
Raw data processed per modality
Modality based derived assets combined after processing is complete
Pipeline modality N
 \ No newline at end of file From 46ca3f1b37545b44d1ad3cf0b2d43f0cf99d0f6c Mon Sep 17 00:00:00 2001 From: Arielle Leon Date: Thu, 4 Jun 2026 17:00:42 -0700 Subject: [PATCH 03/12] chore; adjust layout --- .../diagrams/mid_level/codeocean_pipeline_diagram.drawio | 6 +++--- .../diagrams/mid_level/codeocean_pipeline_diagram.svg | 2 +- 2 files changed, 4 insertions(+), 4 deletions(-) diff --git a/docs/source/diagrams/mid_level/codeocean_pipeline_diagram.drawio b/docs/source/diagrams/mid_level/codeocean_pipeline_diagram.drawio index fff75d0..0eb4d54 100644 --- a/docs/source/diagrams/mid_level/codeocean_pipeline_diagram.drawio +++ b/docs/source/diagrams/mid_level/codeocean_pipeline_diagram.drawio @@ -1,6 +1,6 @@ - + @@ -19,7 +19,7 @@ - + @@ -283,7 +283,7 @@ - + diff --git a/docs/source/diagrams/mid_level/codeocean_pipeline_diagram.svg b/docs/source/diagrams/mid_level/codeocean_pipeline_diagram.svg index d4977f3..775626b 100644 --- a/docs/source/diagrams/mid_level/codeocean_pipeline_diagram.svg +++ b/docs/source/diagrams/mid_level/codeocean_pipeline_diagram.svg @@ -1,4 +1,4 @@ -
Pipeline Modality 1
DocDB
S3: aind-open-data
Pipeline Modality 2
pipeline modality 3
NWB File
a/ND schematized metadata
a/ND schematized metadata includes :
  • procedures.json
  • subject.json
  • data_description.json
  • processing.json
  • data_description.json
  • acquisition.json
  • instrument.json
a/ND schematized metadata
Raw Data
DocDB
S3: aind-open-data
DocDB
S3: aind-open-data
a/ND schematized metadata
Raw Data
Extract, process and package data
QC data in NWB file
quality_control.json
Plots
NWB File
processing.json
processing.json
quality_control.json
data_description.json
NWB File with a/ND Schematized Metadata
Aggregate QC
Aggregate processing
Package schematized metadata into NWB file
Plots and metrics
NWB File
a/ND schematized metadata
Plots and metrics
DocDB
S3: aind-open-data
NWB File
a/ND schematized metadata
Plots and metrics
NWB File
a/ND schematized metadata
Plots and metrics
NWB File
a/ND schematized metadata
Plots and metrics
Raw data come with one or more modalities
Raw data processed per modality
Modality based derived assets combined after processing is complete
Pipeline modality N
 \ No newline at end of file +
Pipeline Modality 1
DocDB
S3: aind-open-data
Pipeline Modality 2
Pipeline Modality 3
NWB File
a/ND schematized metadata
a/ND schematized metadata includes :
  • procedures.json
  • subject.json
  • data_description.json
  • processing.json
  • data_description.json
  • acquisition.json
  • instrument.json
a/ND schematized metadata
Raw Data
DocDB
S3: aind-open-data
DocDB
S3: aind-open-data
a/ND schematized metadata
Raw Data
Extract, process and package data
QC data in NWB file
quality_control.json
Plots
NWB File
processing.json
processing.json
quality_control.json
data_description.json
NWB File with a/ND Schematized Metadata
Aggregate QC
Aggregate processing
Package schematized metadata into NWB file
Plots and metrics
NWB File
a/ND schematized metadata
Plots and metrics
DocDB
S3: aind-open-data
NWB File
a/ND schematized metadata
Plots and metrics
NWB File
a/ND schematized metadata
Plots and metrics
NWB File
a/ND schematized metadata
Plots and metrics
Raw data come with one or more modalities
Raw data processed per modality
Modality based derived assets combined after processing is complete
Pipeline modality N
 \ No newline at end of file From a17439e141ef7a1e22542e6d9ebf270f5ae884cf Mon Sep 17 00:00:00 2001 From: Arielle Leon Date: Thu, 4 Jun 2026 17:06:18 -0700 Subject: [PATCH 04/12] chore: remove extra arrow --- .../diagrams/mid_level/codeocean_pipeline_diagram.drawio | 6 ------ .../diagrams/mid_level/codeocean_pipeline_diagram.svg | 2 +- 2 files changed, 1 insertion(+), 7 deletions(-) diff --git a/docs/source/diagrams/mid_level/codeocean_pipeline_diagram.drawio b/docs/source/diagrams/mid_level/codeocean_pipeline_diagram.drawio index 0eb4d54..5e14e18 100644 --- a/docs/source/diagrams/mid_level/codeocean_pipeline_diagram.drawio +++ b/docs/source/diagrams/mid_level/codeocean_pipeline_diagram.drawio @@ -172,12 +172,6 @@ - - - - - - diff --git a/docs/source/diagrams/mid_level/codeocean_pipeline_diagram.svg b/docs/source/diagrams/mid_level/codeocean_pipeline_diagram.svg index 775626b..7eb3eea 100644 --- a/docs/source/diagrams/mid_level/codeocean_pipeline_diagram.svg +++ b/docs/source/diagrams/mid_level/codeocean_pipeline_diagram.svg @@ -1,4 +1,4 @@ -
Pipeline Modality 1
DocDB
S3: aind-open-data
Pipeline Modality 2
Pipeline Modality 3
NWB File
a/ND schematized metadata
a/ND schematized metadata includes :
  • procedures.json
  • subject.json
  • data_description.json
  • processing.json
  • data_description.json
  • acquisition.json
  • instrument.json
a/ND schematized metadata
Raw Data
DocDB
S3: aind-open-data
DocDB
S3: aind-open-data
a/ND schematized metadata
Raw Data
Extract, process and package data
QC data in NWB file
quality_control.json
Plots
NWB File
processing.json
processing.json
quality_control.json
data_description.json
NWB File with a/ND Schematized Metadata
Aggregate QC
Aggregate processing
Package schematized metadata into NWB file
Plots and metrics
NWB File
a/ND schematized metadata
Plots and metrics
DocDB
S3: aind-open-data
NWB File
a/ND schematized metadata
Plots and metrics
NWB File
a/ND schematized metadata
Plots and metrics
NWB File
a/ND schematized metadata
Plots and metrics
Raw data come with one or more modalities
Raw data processed per modality
Modality based derived assets combined after processing is complete
Pipeline modality N
 \ No newline at end of file +
Pipeline Modality 1
DocDB
S3: aind-open-data
Pipeline Modality 2
Pipeline Modality 3
NWB File
a/ND schematized metadata
a/ND schematized metadata includes :
  • procedures.json
  • subject.json
  • data_description.json
  • processing.json
  • data_description.json
  • acquisition.json
  • instrument.json
a/ND schematized metadata
Raw Data
DocDB
S3: aind-open-data
DocDB
S3: aind-open-data
a/ND schematized metadata
Raw Data
Extract, process and package data
QC data in NWB file
quality_control.json
Plots
NWB File
processing.json
processing.json
quality_control.json
data_description.json
NWB File with a/ND Schematized Metadata
Aggregate QC
Aggregate processing
Package schematized metadata into NWB file
Plots and metrics
NWB File
a/ND schematized metadata
Plots and metrics
DocDB
S3: aind-open-data
NWB File
a/ND schematized metadata
Plots and metrics
NWB File
a/ND schematized metadata
Plots and metrics
NWB File
a/ND schematized metadata
Plots and metrics
Raw data come with one or more modalities
Raw data processed per modality
Modality based derived assets combined after processing is complete
Pipeline modality N
 \ No newline at end of file From f108e9c7517b799c0da0b3b454a5d7c64e30f5e6 Mon Sep 17 00:00:00 2001 From: Arielle Leon Date: Thu, 4 Jun 2026 17:58:33 -0700 Subject: [PATCH 05/12] chore: demonstrate modality separation better --- .../codeocean_pipeline_diagram.drawio | 125 +++++++++++++----- .../mid_level/codeocean_pipeline_diagram.svg | 2 +- 2 files changed, 96 insertions(+), 31 deletions(-) diff --git a/docs/source/diagrams/mid_level/codeocean_pipeline_diagram.drawio b/docs/source/diagrams/mid_level/codeocean_pipeline_diagram.drawio index 5e14e18..84cc559 100644 --- a/docs/source/diagrams/mid_level/codeocean_pipeline_diagram.drawio +++ b/docs/source/diagrams/mid_level/codeocean_pipeline_diagram.drawio @@ -1,6 +1,6 @@ - + @@ -11,16 +11,16 @@ - + - + - + @@ -29,13 +29,10 @@ - - - - + - + @@ -44,16 +41,10 @@ - + - - - - - - - + @@ -181,20 +172,20 @@ - + - + - - + + - + @@ -255,14 +246,8 @@ - - - - - - - - + + @@ -279,6 +264,86 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + diff --git a/docs/source/diagrams/mid_level/codeocean_pipeline_diagram.svg b/docs/source/diagrams/mid_level/codeocean_pipeline_diagram.svg index 7eb3eea..a4c1cc9 100644 --- a/docs/source/diagrams/mid_level/codeocean_pipeline_diagram.svg +++ b/docs/source/diagrams/mid_level/codeocean_pipeline_diagram.svg @@ -1,4 +1,4 @@ -
Pipeline Modality 1
DocDB
S3: aind-open-data
Pipeline Modality 2
Pipeline Modality 3
NWB File
a/ND schematized metadata
a/ND schematized metadata includes :
  • procedures.json
  • subject.json
  • data_description.json
  • processing.json
  • data_description.json
  • acquisition.json
  • instrument.json
a/ND schematized metadata
Raw Data
DocDB
S3: aind-open-data
DocDB
S3: aind-open-data
a/ND schematized metadata
Raw Data
Extract, process and package data
QC data in NWB file
quality_control.json
Plots
NWB File
processing.json
processing.json
quality_control.json
data_description.json
NWB File with a/ND Schematized Metadata
Aggregate QC
Aggregate processing
Package schematized metadata into NWB file
Plots and metrics
NWB File
a/ND schematized metadata
Plots and metrics
DocDB
S3: aind-open-data
NWB File
a/ND schematized metadata
Plots and metrics
NWB File
a/ND schematized metadata
Plots and metrics
NWB File
a/ND schematized metadata
Plots and metrics
Raw data come with one or more modalities
Raw data processed per modality
Modality based derived assets combined after processing is complete
Pipeline modality N
 \ No newline at end of file +
Pipeline Modality 1
DocDB
S3: aind-open-data
Pipeline Modality 2
Pipeline Modality 3
NWB File
a/ND schematized metadata
a/ND schematized metadata includes :
  • procedures.json
  • subject.json
  • data_description.json
  • processing.json
  • data_description.json
  • acquisition.json
  • instrument.json
Raw Data
DocDB
S3: aind-open-data
DocDB
S3: aind-open-data
Extract, process and package data
QC data in NWB file
quality_control.json
Plots
NWB File
processing.json
processing.json
quality_control.json
data_description.json
NWB File with a/ND Schematized Metadata
Aggregate QC
Aggregate processing
Package schematized metadata into NWB file
Plots and metrics
NWB File
a/ND schematized metadata
Plots and metrics
DocDB
S3: aind-open-data
NWB File
a/ND schematized metadata
Plots and metrics
NWB File
a/ND schematized metadata
Plots and metrics
NWB File
a/ND schematized metadata
Plots and metrics
Combine to final data product
Pipeline modality N
a/ND schematized metadata
Raw Data
modality1
modality2%3CmxGraphModel%3E%3Croot%3E%3CmxCell%20id%3D%220%22%2F%3E%3CmxCell%20id%3D%221%22%20parent%3D%220%22%2F%3E%3CmxCell%20id%3D%222%22%20parent%3D%221%22%20style%3D%22html%3D1%3BverticalLabelPosition%3Dbottom%3Balign%3Dcenter%3BlabelBackgroundColor%3D%23ffffff%3BverticalAlign%3Dtop%3BstrokeWidth%3D2%3BstrokeColor%3D%230080F0%3Bshadow%3D0%3Bdashed%3D0%3Bshape%3Dmxgraph.ios7.icons.folder%3B%22%20value%3D%22modality1%22%20vertex%3D%221%22%3E%3CmxGeometry%20height%3D%22130%22%20width%3D%22200%22%20x%3D%22-550%22%20y%3D%22-100%22%20as%3D%22geometry%22%2F%3E%3C%2FmxCell%3E%3C%2Froot%3E%3C%2FmxGraphModel%3E
modality3
metadata
metadata
metadata
a/ND schematized metadata
modality1
metadata
modality2%3CmxGraphModel%3E%3Croot%3E%3CmxCell%20id%3D%220%22%2F%3E%3CmxCell%20id%3D%221%22%20parent%3D%220%22%2F%3E%3CmxCell%20id%3D%222%22%20parent%3D%221%22%20style%3D%22html%3D1%3BverticalLabelPosition%3Dbottom%3Balign%3Dcenter%3BlabelBackgroundColor%3D%23ffffff%3BverticalAlign%3Dtop%3BstrokeWidth%3D2%3BstrokeColor%3D%230080F0%3Bshadow%3D0%3Bdashed%3D0%3Bshape%3Dmxgraph.ios7.icons.folder%3B%22%20value%3D%22modality1%22%20vertex%3D%221%22%3E%3CmxGeometry%20height%3D%22130%22%20width%3D%22200%22%20x%3D%22-550%22%20y%3D%22-100%22%20as%3D%22geometry%22%2F%3E%3C%2FmxCell%3E%3C%2Froot%3E%3C%2FmxGraphModel%3E
metadata
modality3
metadata
 \ No newline at end of file From 316348c8f7d655cbff44ef2d6059f8769c540ab7 Mon Sep 17 00:00:00 2001 From: Arielle Leon Date: Thu, 4 Jun 2026 18:00:03 -0700 Subject: [PATCH 06/12] chore: centering --- .../codeocean_pipeline_diagram.drawio | 26 +++++++++---------- .../mid_level/codeocean_pipeline_diagram.svg | 2 +- 2 files changed, 14 insertions(+), 14 deletions(-) diff --git a/docs/source/diagrams/mid_level/codeocean_pipeline_diagram.drawio b/docs/source/diagrams/mid_level/codeocean_pipeline_diagram.drawio index 84cc559..838e2c9 100644 --- a/docs/source/diagrams/mid_level/codeocean_pipeline_diagram.drawio +++ b/docs/source/diagrams/mid_level/codeocean_pipeline_diagram.drawio @@ -11,10 +11,10 @@ - + - + @@ -32,7 +32,7 @@ - + @@ -291,7 +291,7 @@ - + @@ -318,31 +318,31 @@ - + - + - + - + - + - + - + - + - + diff --git a/docs/source/diagrams/mid_level/codeocean_pipeline_diagram.svg b/docs/source/diagrams/mid_level/codeocean_pipeline_diagram.svg index a4c1cc9..106c632 100644 --- a/docs/source/diagrams/mid_level/codeocean_pipeline_diagram.svg +++ b/docs/source/diagrams/mid_level/codeocean_pipeline_diagram.svg @@ -1,4 +1,4 @@ -
Pipeline Modality 1
DocDB
S3: aind-open-data
Pipeline Modality 2
Pipeline Modality 3
NWB File
a/ND schematized metadata
a/ND schematized metadata includes :
  • procedures.json
  • subject.json
  • data_description.json
  • processing.json
  • data_description.json
  • acquisition.json
  • instrument.json
Raw Data
DocDB
S3: aind-open-data
DocDB
S3: aind-open-data
Extract, process and package data
QC data in NWB file
quality_control.json
Plots
NWB File
processing.json
processing.json
quality_control.json
data_description.json
NWB File with a/ND Schematized Metadata
Aggregate QC
Aggregate processing
Package schematized metadata into NWB file
Plots and metrics
NWB File
a/ND schematized metadata
Plots and metrics
DocDB
S3: aind-open-data
NWB File
a/ND schematized metadata
Plots and metrics
NWB File
a/ND schematized metadata
Plots and metrics
NWB File
a/ND schematized metadata
Plots and metrics
Combine to final data product
Pipeline modality N
a/ND schematized metadata
Raw Data
modality1
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modality3
metadata
metadata
metadata
a/ND schematized metadata
modality1
metadata
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metadata
modality3
metadata
 \ No newline at end of file +
Pipeline Modality 1
DocDB
S3: aind-open-data
Pipeline Modality 2
Pipeline Modality 3
NWB File
a/ND schematized metadata
a/ND schematized metadata includes :
  • procedures.json
  • subject.json
  • data_description.json
  • processing.json
  • data_description.json
  • acquisition.json
  • instrument.json
Raw Data
DocDB
S3: aind-open-data
DocDB
S3: aind-open-data
Extract, process and package data
QC data in NWB file
quality_control.json
Plots
NWB File
processing.json
processing.json
quality_control.json
data_description.json
NWB File with a/ND Schematized Metadata
Aggregate QC
Aggregate processing
Package schematized metadata into NWB file
Plots and metrics
NWB File
a/ND schematized metadata
Plots and metrics
DocDB
S3: aind-open-data
NWB File
a/ND schematized metadata
Plots and metrics
NWB File
a/ND schematized metadata
Plots and metrics
NWB File
a/ND schematized metadata
Plots and metrics
Combine to final data product
Pipeline modality N
a/ND schematized metadata
Raw Data
modality1
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modality3
metadata
metadata
metadata
a/ND schematized metadata
modality1
metadata
modality2%3CmxGraphModel%3E%3Croot%3E%3CmxCell%20id%3D%220%22%2F%3E%3CmxCell%20id%3D%221%22%20parent%3D%220%22%2F%3E%3CmxCell%20id%3D%222%22%20parent%3D%221%22%20style%3D%22html%3D1%3BverticalLabelPosition%3Dbottom%3Balign%3Dcenter%3BlabelBackgroundColor%3D%23ffffff%3BverticalAlign%3Dtop%3BstrokeWidth%3D2%3BstrokeColor%3D%230080F0%3Bshadow%3D0%3Bdashed%3D0%3Bshape%3Dmxgraph.ios7.icons.folder%3B%22%20value%3D%22modality1%22%20vertex%3D%221%22%3E%3CmxGeometry%20height%3D%22130%22%20width%3D%22200%22%20x%3D%22-550%22%20y%3D%22-100%22%20as%3D%22geometry%22%2F%3E%3C%2FmxCell%3E%3C%2Froot%3E%3C%2FmxGraphModel%3E
metadata
modality3
metadata
 \ No newline at end of file From cbc46114dc8ed50ce79692410f19952005a15fd3 Mon Sep 17 00:00:00 2001 From: Arielle Leon Date: Fri, 5 Jun 2026 09:59:09 -0700 Subject: [PATCH 07/12] chore: change color schema and recentering --- .../codeocean_pipeline_diagram.drawio | 64 +++++++++---------- .../mid_level/codeocean_pipeline_diagram.svg | 2 +- 2 files changed, 32 insertions(+), 34 deletions(-) diff --git a/docs/source/diagrams/mid_level/codeocean_pipeline_diagram.drawio b/docs/source/diagrams/mid_level/codeocean_pipeline_diagram.drawio index 838e2c9..b5cae58 100644 --- a/docs/source/diagrams/mid_level/codeocean_pipeline_diagram.drawio +++ b/docs/source/diagrams/mid_level/codeocean_pipeline_diagram.drawio @@ -1,10 +1,10 @@ - + - + @@ -22,23 +22,23 @@ - + - + - + - + @@ -46,8 +46,9 @@ - - + + + @@ -58,7 +59,7 @@ - + @@ -74,7 +75,7 @@ - + @@ -92,33 +93,33 @@ - + - + - + - + - + - + @@ -126,19 +127,19 @@ - + - + - + - + @@ -198,31 +199,31 @@ - + - + - + - + - + - + @@ -246,13 +247,10 @@ - - - - - + + @@ -261,8 +259,8 @@ - - + + diff --git a/docs/source/diagrams/mid_level/codeocean_pipeline_diagram.svg b/docs/source/diagrams/mid_level/codeocean_pipeline_diagram.svg index 106c632..a0a319c 100644 --- a/docs/source/diagrams/mid_level/codeocean_pipeline_diagram.svg +++ b/docs/source/diagrams/mid_level/codeocean_pipeline_diagram.svg @@ -1,4 +1,4 @@ -
Pipeline Modality 1
DocDB
S3: aind-open-data
Pipeline Modality 2
Pipeline Modality 3
NWB File
a/ND schematized metadata
a/ND schematized metadata includes :
  • procedures.json
  • subject.json
  • data_description.json
  • processing.json
  • data_description.json
  • acquisition.json
  • instrument.json
Raw Data
DocDB
S3: aind-open-data
DocDB
S3: aind-open-data
Extract, process and package data
QC data in NWB file
quality_control.json
Plots
NWB File
processing.json
processing.json
quality_control.json
data_description.json
NWB File with a/ND Schematized Metadata
Aggregate QC
Aggregate processing
Package schematized metadata into NWB file
Plots and metrics
NWB File
a/ND schematized metadata
Plots and metrics
DocDB
S3: aind-open-data
NWB File
a/ND schematized metadata
Plots and metrics
NWB File
a/ND schematized metadata
Plots and metrics
NWB File
a/ND schematized metadata
Plots and metrics
Combine to final data product
Pipeline modality N
a/ND schematized metadata
Raw Data
modality1
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modality3
metadata
metadata
metadata
a/ND schematized metadata
modality1
metadata
modality2%3CmxGraphModel%3E%3Croot%3E%3CmxCell%20id%3D%220%22%2F%3E%3CmxCell%20id%3D%221%22%20parent%3D%220%22%2F%3E%3CmxCell%20id%3D%222%22%20parent%3D%221%22%20style%3D%22html%3D1%3BverticalLabelPosition%3Dbottom%3Balign%3Dcenter%3BlabelBackgroundColor%3D%23ffffff%3BverticalAlign%3Dtop%3BstrokeWidth%3D2%3BstrokeColor%3D%230080F0%3Bshadow%3D0%3Bdashed%3D0%3Bshape%3Dmxgraph.ios7.icons.folder%3B%22%20value%3D%22modality1%22%20vertex%3D%221%22%3E%3CmxGeometry%20height%3D%22130%22%20width%3D%22200%22%20x%3D%22-550%22%20y%3D%22-100%22%20as%3D%22geometry%22%2F%3E%3C%2FmxCell%3E%3C%2Froot%3E%3C%2FmxGraphModel%3E
metadata
modality3
metadata
 \ No newline at end of file +
Pipeline Modality 1
DocDB
S3: aind-open-data
Pipeline Modality 2
Pipeline Modality 3
NWB File
a/ND schematized metadata
a/ND schematized metadata includes :
  • procedures.json
  • subject.json
  • data_description.json
  • processing.json
  • data_description.json
  • acquisition.json
  • instrument.json
Raw Data
DocDB
S3: aind-open-data
DocDB
S3: aind-open-data
Extract, process and package data
QC data in NWB file
quality_control.json
Plots
NWB File
processing.json
processing.json
quality_control.json
data_description.json
NWB File with a/ND Schematized Metadata
Aggregate QC
Aggregate processing
Package schematized metadata into NWB file
Plots and metrics
NWB File
a/ND schematized metadata
Plots and metrics
DocDB
S3: aind-open-data
NWB File
a/ND schematized metadata
Plots and metrics
NWB File
a/ND schematized metadata
Plots and metrics
NWB File
a/ND schematized metadata
Plots and metrics
Pipeline modality N
a/ND schematized metadata
Raw Data
modality1
modality2%3CmxGraphModel%3E%3Croot%3E%3CmxCell%20id%3D%220%22%2F%3E%3CmxCell%20id%3D%221%22%20parent%3D%220%22%2F%3E%3CmxCell%20id%3D%222%22%20parent%3D%221%22%20style%3D%22html%3D1%3BverticalLabelPosition%3Dbottom%3Balign%3Dcenter%3BlabelBackgroundColor%3D%23ffffff%3BverticalAlign%3Dtop%3BstrokeWidth%3D2%3BstrokeColor%3D%230080F0%3Bshadow%3D0%3Bdashed%3D0%3Bshape%3Dmxgraph.ios7.icons.folder%3B%22%20value%3D%22modality1%22%20vertex%3D%221%22%3E%3CmxGeometry%20height%3D%22130%22%20width%3D%22200%22%20x%3D%22-550%22%20y%3D%22-100%22%20as%3D%22geometry%22%2F%3E%3C%2FmxCell%3E%3C%2Froot%3E%3C%2FmxGraphModel%3E
modality3
metadata
metadata
metadata
a/ND schematized metadata
modality1
metadata
modality2%3CmxGraphModel%3E%3Croot%3E%3CmxCell%20id%3D%220%22%2F%3E%3CmxCell%20id%3D%221%22%20parent%3D%220%22%2F%3E%3CmxCell%20id%3D%222%22%20parent%3D%221%22%20style%3D%22html%3D1%3BverticalLabelPosition%3Dbottom%3Balign%3Dcenter%3BlabelBackgroundColor%3D%23ffffff%3BverticalAlign%3Dtop%3BstrokeWidth%3D2%3BstrokeColor%3D%230080F0%3Bshadow%3D0%3Bdashed%3D0%3Bshape%3Dmxgraph.ios7.icons.folder%3B%22%20value%3D%22modality1%22%20vertex%3D%221%22%3E%3CmxGeometry%20height%3D%22130%22%20width%3D%22200%22%20x%3D%22-550%22%20y%3D%22-100%22%20as%3D%22geometry%22%2F%3E%3C%2FmxCell%3E%3C%2Froot%3E%3C%2FmxGraphModel%3E
metadata
modality3
metadata
 \ No newline at end of file From 53f9efacc47654fa7f3f940bc1d12997d1493e01 Mon Sep 17 00:00:00 2001 From: Arielle Leon Date: Fri, 5 Jun 2026 16:46:38 -0700 Subject: [PATCH 08/12] chore: rename metadata to reference aind-data-schema --- .../mid_level/codeocean_pipeline_diagram.drawio | 16 ++++++++-------- .../mid_level/codeocean_pipeline_diagram.svg | 2 +- 2 files changed, 9 insertions(+), 9 deletions(-) diff --git a/docs/source/diagrams/mid_level/codeocean_pipeline_diagram.drawio b/docs/source/diagrams/mid_level/codeocean_pipeline_diagram.drawio index b5cae58..478a5fb 100644 --- a/docs/source/diagrams/mid_level/codeocean_pipeline_diagram.drawio +++ b/docs/source/diagrams/mid_level/codeocean_pipeline_diagram.drawio @@ -1,6 +1,6 @@ - + @@ -25,10 +25,10 @@ - + - + @@ -202,7 +202,7 @@ - + @@ -211,7 +211,7 @@ - + @@ -220,7 +220,7 @@ - + @@ -288,7 +288,7 @@ - + @@ -313,7 +313,7 @@ - + diff --git a/docs/source/diagrams/mid_level/codeocean_pipeline_diagram.svg b/docs/source/diagrams/mid_level/codeocean_pipeline_diagram.svg index a0a319c..d125c0c 100644 --- a/docs/source/diagrams/mid_level/codeocean_pipeline_diagram.svg +++ b/docs/source/diagrams/mid_level/codeocean_pipeline_diagram.svg @@ -1,4 +1,4 @@ -
Pipeline Modality 1
DocDB
S3: aind-open-data
Pipeline Modality 2
Pipeline Modality 3
NWB File
a/ND schematized metadata
a/ND schematized metadata includes :
  • procedures.json
  • subject.json
  • data_description.json
  • processing.json
  • data_description.json
  • acquisition.json
  • instrument.json
Raw Data
DocDB
S3: aind-open-data
DocDB
S3: aind-open-data
Extract, process and package data
QC data in NWB file
quality_control.json
Plots
NWB File
processing.json
processing.json
quality_control.json
data_description.json
NWB File with a/ND Schematized Metadata
Aggregate QC
Aggregate processing
Package schematized metadata into NWB file
Plots and metrics
NWB File
a/ND schematized metadata
Plots and metrics
DocDB
S3: aind-open-data
NWB File
a/ND schematized metadata
Plots and metrics
NWB File
a/ND schematized metadata
Plots and metrics
NWB File
a/ND schematized metadata
Plots and metrics
Pipeline modality N
a/ND schematized metadata
Raw Data
modality1
modality2%3CmxGraphModel%3E%3Croot%3E%3CmxCell%20id%3D%220%22%2F%3E%3CmxCell%20id%3D%221%22%20parent%3D%220%22%2F%3E%3CmxCell%20id%3D%222%22%20parent%3D%221%22%20style%3D%22html%3D1%3BverticalLabelPosition%3Dbottom%3Balign%3Dcenter%3BlabelBackgroundColor%3D%23ffffff%3BverticalAlign%3Dtop%3BstrokeWidth%3D2%3BstrokeColor%3D%230080F0%3Bshadow%3D0%3Bdashed%3D0%3Bshape%3Dmxgraph.ios7.icons.folder%3B%22%20value%3D%22modality1%22%20vertex%3D%221%22%3E%3CmxGeometry%20height%3D%22130%22%20width%3D%22200%22%20x%3D%22-550%22%20y%3D%22-100%22%20as%3D%22geometry%22%2F%3E%3C%2FmxCell%3E%3C%2Froot%3E%3C%2FmxGraphModel%3E
modality3
metadata
metadata
metadata
a/ND schematized metadata
modality1
metadata
modality2%3CmxGraphModel%3E%3Croot%3E%3CmxCell%20id%3D%220%22%2F%3E%3CmxCell%20id%3D%221%22%20parent%3D%220%22%2F%3E%3CmxCell%20id%3D%222%22%20parent%3D%221%22%20style%3D%22html%3D1%3BverticalLabelPosition%3Dbottom%3Balign%3Dcenter%3BlabelBackgroundColor%3D%23ffffff%3BverticalAlign%3Dtop%3BstrokeWidth%3D2%3BstrokeColor%3D%230080F0%3Bshadow%3D0%3Bdashed%3D0%3Bshape%3Dmxgraph.ios7.icons.folder%3B%22%20value%3D%22modality1%22%20vertex%3D%221%22%3E%3CmxGeometry%20height%3D%22130%22%20width%3D%22200%22%20x%3D%22-550%22%20y%3D%22-100%22%20as%3D%22geometry%22%2F%3E%3C%2FmxCell%3E%3C%2Froot%3E%3C%2FmxGraphModel%3E
metadata
modality3
metadata
 \ No newline at end of file +
Pipeline Modality 1
DocDB
S3: aind-open-data
Pipeline Modality 2
Pipeline Modality 3
NWB File
aind-data-schema metadata
aind-data-schema metadata:
  • procedures.json
  • subject.json
  • data_description.json
  • processing.json
  • data_description.json
  • acquisition.json
  • instrument.json
Raw Data
DocDB
S3: aind-open-data
DocDB
S3: aind-open-data
Extract, process and package data
QC data in NWB file
quality_control.json
Plots
NWB File
processing.json
processing.json
quality_control.json
data_description.json
NWB File with a/ND Schematized Metadata
Aggregate QC
Aggregate processing
Package schematized metadata into NWB file
Plots and metrics
NWB File
a/ND schematized metadata
Plots and metrics
DocDB
S3: aind-open-data
NWB File
aind-data-schema metadata
Plots and metrics
NWB File
aind-data-schema metadata
Plots and metrics
NWB File
aind-data-schema metadata
Plots and metrics
Pipeline modality N
aind-data-schema metadata
Raw Data
modality1
modality2%3CmxGraphModel%3E%3Croot%3E%3CmxCell%20id%3D%220%22%2F%3E%3CmxCell%20id%3D%221%22%20parent%3D%220%22%2F%3E%3CmxCell%20id%3D%222%22%20parent%3D%221%22%20style%3D%22html%3D1%3BverticalLabelPosition%3Dbottom%3Balign%3Dcenter%3BlabelBackgroundColor%3D%23ffffff%3BverticalAlign%3Dtop%3BstrokeWidth%3D2%3BstrokeColor%3D%230080F0%3Bshadow%3D0%3Bdashed%3D0%3Bshape%3Dmxgraph.ios7.icons.folder%3B%22%20value%3D%22modality1%22%20vertex%3D%221%22%3E%3CmxGeometry%20height%3D%22130%22%20width%3D%22200%22%20x%3D%22-550%22%20y%3D%22-100%22%20as%3D%22geometry%22%2F%3E%3C%2FmxCell%3E%3C%2Froot%3E%3C%2FmxGraphModel%3E
modality3
metadata
metadata
metadata
a/ND schematized metadata
modality1
metadata
modality2%3CmxGraphModel%3E%3Croot%3E%3CmxCell%20id%3D%220%22%2F%3E%3CmxCell%20id%3D%221%22%20parent%3D%220%22%2F%3E%3CmxCell%20id%3D%222%22%20parent%3D%221%22%20style%3D%22html%3D1%3BverticalLabelPosition%3Dbottom%3Balign%3Dcenter%3BlabelBackgroundColor%3D%23ffffff%3BverticalAlign%3Dtop%3BstrokeWidth%3D2%3BstrokeColor%3D%230080F0%3Bshadow%3D0%3Bdashed%3D0%3Bshape%3Dmxgraph.ios7.icons.folder%3B%22%20value%3D%22modality1%22%20vertex%3D%221%22%3E%3CmxGeometry%20height%3D%22130%22%20width%3D%22200%22%20x%3D%22-550%22%20y%3D%22-100%22%20as%3D%22geometry%22%2F%3E%3C%2FmxCell%3E%3C%2Froot%3E%3C%2FmxGraphModel%3E
metadata
modality3
metadata
 \ No newline at end of file From 8971cfee2570b98e56815991374971b7c041ea10 Mon Sep 17 00:00:00 2001 From: Arielle Leon Date: Fri, 5 Jun 2026 16:50:28 -0700 Subject: [PATCH 09/12] chore: rename Plots to Artifacts --- .../diagrams/mid_level/codeocean_pipeline_diagram.drawio | 4 ++-- docs/source/diagrams/mid_level/codeocean_pipeline_diagram.svg | 2 +- 2 files changed, 3 insertions(+), 3 deletions(-) diff --git a/docs/source/diagrams/mid_level/codeocean_pipeline_diagram.drawio b/docs/source/diagrams/mid_level/codeocean_pipeline_diagram.drawio index 478a5fb..411d27e 100644 --- a/docs/source/diagrams/mid_level/codeocean_pipeline_diagram.drawio +++ b/docs/source/diagrams/mid_level/codeocean_pipeline_diagram.drawio @@ -69,7 +69,7 @@ - + @@ -312,7 +312,7 @@ - + diff --git a/docs/source/diagrams/mid_level/codeocean_pipeline_diagram.svg b/docs/source/diagrams/mid_level/codeocean_pipeline_diagram.svg index d125c0c..4a043f3 100644 --- a/docs/source/diagrams/mid_level/codeocean_pipeline_diagram.svg +++ b/docs/source/diagrams/mid_level/codeocean_pipeline_diagram.svg @@ -1,4 +1,4 @@ -
Pipeline Modality 1
DocDB
S3: aind-open-data
Pipeline Modality 2
Pipeline Modality 3
NWB File
aind-data-schema metadata
aind-data-schema metadata:
  • procedures.json
  • subject.json
  • data_description.json
  • processing.json
  • data_description.json
  • acquisition.json
  • instrument.json
Raw Data
DocDB
S3: aind-open-data
DocDB
S3: aind-open-data
Extract, process and package data
QC data in NWB file
quality_control.json
Plots
NWB File
processing.json
processing.json
quality_control.json
data_description.json
NWB File with a/ND Schematized Metadata
Aggregate QC
Aggregate processing
Package schematized metadata into NWB file
Plots and metrics
NWB File
a/ND schematized metadata
Plots and metrics
DocDB
S3: aind-open-data
NWB File
aind-data-schema metadata
Plots and metrics
NWB File
aind-data-schema metadata
Plots and metrics
NWB File
aind-data-schema metadata
Plots and metrics
Pipeline modality N
aind-data-schema metadata
Raw Data
modality1
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metadata
modality3
metadata
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Pipeline Modality 1
DocDB
S3: aind-open-data
Pipeline Modality 2
Pipeline Modality 3
NWB File
aind-data-schema metadata
aind-data-schema metadata:
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Raw Data
DocDB
S3: aind-open-data
DocDB
S3: aind-open-data
Extract, process and package data
QC data in NWB file
quality_control.json
Artifacts
NWB File
processing.json
processing.json
quality_control.json
data_description.json
NWB File with a/ND Schematized Metadata
Aggregate QC
Aggregate processing
Package schematized metadata into NWB file
Plots and metrics
NWB File
a/ND schematized metadata
Plots and metrics
DocDB
S3: aind-open-data
NWB File
aind-data-schema metadata
Plots and metrics
NWB File
aind-data-schema metadata
Plots and metrics
NWB File
aind-data-schema metadata
Plots and metrics
Pipeline modality N
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Raw Data
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modality3
metadata
metadata
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aind-data-schema metadata
modality1
metadata
modality2%3CmxGraphModel%3E%3Croot%3E%3CmxCell%20id%3D%220%22%2F%3E%3CmxCell%20id%3D%221%22%20parent%3D%220%22%2F%3E%3CmxCell%20id%3D%222%22%20parent%3D%221%22%20style%3D%22html%3D1%3BverticalLabelPosition%3Dbottom%3Balign%3Dcenter%3BlabelBackgroundColor%3D%23ffffff%3BverticalAlign%3Dtop%3BstrokeWidth%3D2%3BstrokeColor%3D%230080F0%3Bshadow%3D0%3Bdashed%3D0%3Bshape%3Dmxgraph.ios7.icons.folder%3B%22%20value%3D%22modality1%22%20vertex%3D%221%22%3E%3CmxGeometry%20height%3D%22130%22%20width%3D%22200%22%20x%3D%22-550%22%20y%3D%22-100%22%20as%3D%22geometry%22%2F%3E%3C%2FmxCell%3E%3C%2Froot%3E%3C%2FmxGraphModel%3E
metadata
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 \ No newline at end of file From 462c21dca3347ea9ee060dcbe5fcb7b35f1a7a76 Mon Sep 17 00:00:00 2001 From: Arielle Leon Date: Fri, 5 Jun 2026 21:12:26 -0700 Subject: [PATCH 10/12] chore: refactoring the design of the pipeline innards --- .../codeocean_pipeline_diagram.drawio | 240 +++++++++--------- .../mid_level/codeocean_pipeline_diagram.svg | 2 +- 2 files changed, 118 insertions(+), 124 deletions(-) diff --git a/docs/source/diagrams/mid_level/codeocean_pipeline_diagram.drawio b/docs/source/diagrams/mid_level/codeocean_pipeline_diagram.drawio index 411d27e..3a8d1fd 100644 --- a/docs/source/diagrams/mid_level/codeocean_pipeline_diagram.drawio +++ b/docs/source/diagrams/mid_level/codeocean_pipeline_diagram.drawio @@ -1,12 +1,9 @@ - + - - - @@ -41,128 +38,34 @@ - + - - - - - - - - - - - - - - - - - - - - - + - + - - - - - - - - - - - - - - - - - - - + - - - - - - - - - - - - - - - - - - - - - - - - - - - + - - - - - - - - - - + + - + - + - - - - - - - - - - - - - - - - - - - - - - - + @@ -191,10 +94,10 @@ - + - + @@ -255,13 +158,10 @@ - - + + - - - @@ -292,28 +192,28 @@ - + - + - + - + - + - + - + - + @@ -342,6 +242,100 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + diff --git a/docs/source/diagrams/mid_level/codeocean_pipeline_diagram.svg b/docs/source/diagrams/mid_level/codeocean_pipeline_diagram.svg index 4a043f3..3e6f645 100644 --- a/docs/source/diagrams/mid_level/codeocean_pipeline_diagram.svg +++ b/docs/source/diagrams/mid_level/codeocean_pipeline_diagram.svg @@ -1,4 +1,4 @@ -
Pipeline Modality 1
DocDB
S3: aind-open-data
Pipeline Modality 2
Pipeline Modality 3
NWB File
aind-data-schema metadata
aind-data-schema metadata:
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Raw Data
DocDB
S3: aind-open-data
DocDB
S3: aind-open-data
Extract, process and package data
QC data in NWB file
quality_control.json
Artifacts
NWB File
processing.json
processing.json
quality_control.json
data_description.json
NWB File with a/ND Schematized Metadata
Aggregate QC
Aggregate processing
Package schematized metadata into NWB file
Plots and metrics
NWB File
a/ND schematized metadata
Plots and metrics
DocDB
S3: aind-open-data
NWB File
aind-data-schema metadata
Plots and metrics
NWB File
aind-data-schema metadata
Plots and metrics
NWB File
aind-data-schema metadata
Plots and metrics
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Raw Data
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modality3
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aind-data-schema metadata
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metadata
modality3
metadata
 \ No newline at end of file +
Pipeline Modality 1
DocDB
S3: aind-open-data
Pipeline Modality 2
Pipeline Modality 3
NWB File
aind-data-schema metadata
aind-data-schema metadata:
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  • instrument.json
Raw Data
DocDB
S3: aind-open-data
DocDB
S3: aind-open-data
quality_control.json
Artifacts
data_description.json
NWB File with aind-data-schema metadata
Plots and metrics
NWB File
a/ND schematized metadata
Plots and metrics
DocDB
S3: aind-open-data
NWB File
aind-data-schema metadata
Plots and metrics
NWB File
aind-data-schema metadata
Plots and metrics
NWB File
aind-data-schema metadata
Plots and metrics
aind-data-schema metadata
Raw Data
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modality3
metadata
metadata
metadata
aind-data-schema metadata
modality1
metadata
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metadata
modality3
metadata
NWB File
processing.json
Tranform and Process
QC NWB FFile
Metadata Manager
+
+
+
 \ No newline at end of file From 8730c0c9ffcb53e80df339cf86b687ac698cf447 Mon Sep 17 00:00:00 2001 From: Arielle Leon Date: Fri, 5 Jun 2026 21:37:40 -0700 Subject: [PATCH 11/12] chore: rebalance diagram --- .../codeocean_pipeline_diagram.drawio | 150 +++++++++--------- .../mid_level/codeocean_pipeline_diagram.svg | 2 +- 2 files changed, 76 insertions(+), 76 deletions(-) diff --git a/docs/source/diagrams/mid_level/codeocean_pipeline_diagram.drawio b/docs/source/diagrams/mid_level/codeocean_pipeline_diagram.drawio index 3a8d1fd..e86c58d 100644 --- a/docs/source/diagrams/mid_level/codeocean_pipeline_diagram.drawio +++ b/docs/source/diagrams/mid_level/codeocean_pipeline_diagram.drawio @@ -1,11 +1,11 @@ - + - + @@ -17,13 +17,13 @@ - + - + - + @@ -44,28 +44,28 @@ - + - + - + - + - + - + - - + + - + @@ -77,7 +77,7 @@ - + @@ -87,20 +87,17 @@ - + - + - - - - + @@ -121,18 +118,18 @@ - + - + - + - - + + @@ -143,13 +140,10 @@ - - + + - - - @@ -158,8 +152,8 @@ - - + + @@ -178,13 +172,13 @@ - + - + - + @@ -192,28 +186,28 @@ - + - + - + - + - + - + - + - + @@ -243,98 +237,104 @@ - + - + - + - - + + - - + + - - + + - + - - + + - + - - + + - + - + - - + + - + - - + + - + - - + + - + - - + + - + - + - + + + + + + + diff --git a/docs/source/diagrams/mid_level/codeocean_pipeline_diagram.svg b/docs/source/diagrams/mid_level/codeocean_pipeline_diagram.svg index 3e6f645..527db21 100644 --- a/docs/source/diagrams/mid_level/codeocean_pipeline_diagram.svg +++ b/docs/source/diagrams/mid_level/codeocean_pipeline_diagram.svg @@ -1,4 +1,4 @@ -
Pipeline Modality 1
DocDB
S3: aind-open-data
Pipeline Modality 2
Pipeline Modality 3
NWB File
aind-data-schema metadata
aind-data-schema metadata:
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Raw Data
DocDB
S3: aind-open-data
DocDB
S3: aind-open-data
quality_control.json
Artifacts
data_description.json
NWB File with aind-data-schema metadata
Plots and metrics
NWB File
a/ND schematized metadata
Plots and metrics
DocDB
S3: aind-open-data
NWB File
aind-data-schema metadata
Plots and metrics
NWB File
aind-data-schema metadata
Plots and metrics
NWB File
aind-data-schema metadata
Plots and metrics
aind-data-schema metadata
Raw Data
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modality3
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metadata
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metadata
modality3
metadata
NWB File
processing.json
Tranform and Process
QC NWB FFile
Metadata Manager
+
+
+
 \ No newline at end of file +
Pipeline Modality 1
DocDB
S3: aind-open-data
Pipeline Modality 2
Pipeline Modality 3
NWB File
aind-data-schema metadata
aind-data-schema metadata:
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  • subject.json
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  • processing.json
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  • instrument.json
Raw Data
DocDB
S3: aind-open-data
DocDB
S3: aind-open-data
quality_control.json
Artifacts
data_description.json
NWB File with aind-data-schema metadata
Plots and metrics
NWB File
aind-data-schema metadata
Plots and metrics
DocDB
S3: aind-open-data
NWB File
aind-data-schema metadata
Plots and metrics
NWB File
aind-data-schema metadata
Plots and metrics
NWB File
aind-data-schema metadata
Plots and metrics
aind-data-schema metadata
Raw Data
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modality3
metadata
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metadata
aind-data-schema metadata
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metadata
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metadata
modality3
metadata
NWB File
processing.json
Tranform and Process
QC NWB FFile
Metadata Manager
+
+
+
 \ No newline at end of file From 6c4b9e5504c8688a173462598b30a4ce6bbad5a9 Mon Sep 17 00:00:00 2001 From: Arielle Leon Date: Wed, 10 Jun 2026 13:51:19 -0700 Subject: [PATCH 12/12] chore: remove individual metadata from modality representation --- .../codeocean_pipeline_diagram.drawio | 20 +------------------ .../mid_level/codeocean_pipeline_diagram.svg | 2 +- 2 files changed, 2 insertions(+), 20 deletions(-) diff --git a/docs/source/diagrams/mid_level/codeocean_pipeline_diagram.drawio b/docs/source/diagrams/mid_level/codeocean_pipeline_diagram.drawio index e86c58d..e0906e9 100644 --- a/docs/source/diagrams/mid_level/codeocean_pipeline_diagram.drawio +++ b/docs/source/diagrams/mid_level/codeocean_pipeline_diagram.drawio @@ -1,6 +1,6 @@ - + @@ -209,33 +209,15 @@ - - - - - - - - - - - - - - - - - - diff --git a/docs/source/diagrams/mid_level/codeocean_pipeline_diagram.svg b/docs/source/diagrams/mid_level/codeocean_pipeline_diagram.svg index 527db21..04e9480 100644 --- a/docs/source/diagrams/mid_level/codeocean_pipeline_diagram.svg +++ b/docs/source/diagrams/mid_level/codeocean_pipeline_diagram.svg @@ -1,4 +1,4 @@ -
Pipeline Modality 1
DocDB
S3: aind-open-data
Pipeline Modality 2
Pipeline Modality 3
NWB File
aind-data-schema metadata
aind-data-schema metadata:
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  • processing.json
  • data_description.json
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  • instrument.json
Raw Data
DocDB
S3: aind-open-data
DocDB
S3: aind-open-data
quality_control.json
Artifacts
data_description.json
NWB File with aind-data-schema metadata
Plots and metrics
NWB File
aind-data-schema metadata
Plots and metrics
DocDB
S3: aind-open-data
NWB File
aind-data-schema metadata
Plots and metrics
NWB File
aind-data-schema metadata
Plots and metrics
NWB File
aind-data-schema metadata
Plots and metrics
aind-data-schema metadata
Raw Data
modality1
modality2%3CmxGraphModel%3E%3Croot%3E%3CmxCell%20id%3D%220%22%2F%3E%3CmxCell%20id%3D%221%22%20parent%3D%220%22%2F%3E%3CmxCell%20id%3D%222%22%20parent%3D%221%22%20style%3D%22html%3D1%3BverticalLabelPosition%3Dbottom%3Balign%3Dcenter%3BlabelBackgroundColor%3D%23ffffff%3BverticalAlign%3Dtop%3BstrokeWidth%3D2%3BstrokeColor%3D%230080F0%3Bshadow%3D0%3Bdashed%3D0%3Bshape%3Dmxgraph.ios7.icons.folder%3B%22%20value%3D%22modality1%22%20vertex%3D%221%22%3E%3CmxGeometry%20height%3D%22130%22%20width%3D%22200%22%20x%3D%22-550%22%20y%3D%22-100%22%20as%3D%22geometry%22%2F%3E%3C%2FmxCell%3E%3C%2Froot%3E%3C%2FmxGraphModel%3E
modality3
metadata
metadata
metadata
aind-data-schema metadata
modality1
metadata
modality2%3CmxGraphModel%3E%3Croot%3E%3CmxCell%20id%3D%220%22%2F%3E%3CmxCell%20id%3D%221%22%20parent%3D%220%22%2F%3E%3CmxCell%20id%3D%222%22%20parent%3D%221%22%20style%3D%22html%3D1%3BverticalLabelPosition%3Dbottom%3Balign%3Dcenter%3BlabelBackgroundColor%3D%23ffffff%3BverticalAlign%3Dtop%3BstrokeWidth%3D2%3BstrokeColor%3D%230080F0%3Bshadow%3D0%3Bdashed%3D0%3Bshape%3Dmxgraph.ios7.icons.folder%3B%22%20value%3D%22modality1%22%20vertex%3D%221%22%3E%3CmxGeometry%20height%3D%22130%22%20width%3D%22200%22%20x%3D%22-550%22%20y%3D%22-100%22%20as%3D%22geometry%22%2F%3E%3C%2FmxCell%3E%3C%2Froot%3E%3C%2FmxGraphModel%3E
metadata
modality3
metadata
NWB File
processing.json
Tranform and Process
QC NWB FFile
Metadata Manager
+
+
+
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Pipeline Modality 1
DocDB
S3: aind-open-data
Pipeline Modality 2
Pipeline Modality 3
NWB File
aind-data-schema metadata
aind-data-schema metadata:
  • procedures.json
  • subject.json
  • data_description.json
  • processing.json
  • data_description.json
  • acquisition.json
  • instrument.json
Raw Data
DocDB
S3: aind-open-data
DocDB
S3: aind-open-data
quality_control.json
Artifacts
data_description.json
NWB File with aind-data-schema metadata
Plots and metrics
NWB File
aind-data-schema metadata
Plots and metrics
DocDB
S3: aind-open-data
NWB File
aind-data-schema metadata
Plots and metrics
NWB File
aind-data-schema metadata
Plots and metrics
NWB File
aind-data-schema metadata
Plots and metrics
aind-data-schema metadata
Raw Data
modality1
modality2%3CmxGraphModel%3E%3Croot%3E%3CmxCell%20id%3D%220%22%2F%3E%3CmxCell%20id%3D%221%22%20parent%3D%220%22%2F%3E%3CmxCell%20id%3D%222%22%20parent%3D%221%22%20style%3D%22html%3D1%3BverticalLabelPosition%3Dbottom%3Balign%3Dcenter%3BlabelBackgroundColor%3D%23ffffff%3BverticalAlign%3Dtop%3BstrokeWidth%3D2%3BstrokeColor%3D%230080F0%3Bshadow%3D0%3Bdashed%3D0%3Bshape%3Dmxgraph.ios7.icons.folder%3B%22%20value%3D%22modality1%22%20vertex%3D%221%22%3E%3CmxGeometry%20height%3D%22130%22%20width%3D%22200%22%20x%3D%22-550%22%20y%3D%22-100%22%20as%3D%22geometry%22%2F%3E%3C%2FmxCell%3E%3C%2Froot%3E%3C%2FmxGraphModel%3E
modality3
metadata
metadata
metadata
aind-data-schema metadata
modality1
modality2%3CmxGraphModel%3E%3Croot%3E%3CmxCell%20id%3D%220%22%2F%3E%3CmxCell%20id%3D%221%22%20parent%3D%220%22%2F%3E%3CmxCell%20id%3D%222%22%20parent%3D%221%22%20style%3D%22html%3D1%3BverticalLabelPosition%3Dbottom%3Balign%3Dcenter%3BlabelBackgroundColor%3D%23ffffff%3BverticalAlign%3Dtop%3BstrokeWidth%3D2%3BstrokeColor%3D%230080F0%3Bshadow%3D0%3Bdashed%3D0%3Bshape%3Dmxgraph.ios7.icons.folder%3B%22%20value%3D%22modality1%22%20vertex%3D%221%22%3E%3CmxGeometry%20height%3D%22130%22%20width%3D%22200%22%20x%3D%22-550%22%20y%3D%22-100%22%20as%3D%22geometry%22%2F%3E%3C%2FmxCell%3E%3C%2Froot%3E%3C%2FmxGraphModel%3E
modality3
NWB File
processing.json
Tranform and Process
QC NWB FFile
Metadata Manager
+
+
+
 \ No newline at end of file