diff --git a/CHANGELOG.md b/CHANGELOG.md
index 09ed8718b..1c188a624 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -2,6 +2,7 @@
## v0.0.19 (in progress)
- Directory validation changes for "shared" uploads
+- Update Phenocycler directory schema
## v0.0.18
diff --git a/docs/phenocycler/current/index.md b/docs/phenocycler/current/index.md
index 712f07576..2f41d4176 100644
--- a/docs/phenocycler/current/index.md
+++ b/docs/phenocycler/current/index.md
@@ -46,7 +46,6 @@ Related files:
| raw\/images\/phenocycler\/(?:CoverslipMask.tif|FlowCellOverview.tif|OverviewFL.tif|SampleValMask.tif)
| | Required file from the temp directory generated by the PhenoCycler. The optional files depend on which version of the PhenoCycler software was being used. |
| lab_processed\/.*
| ✓ | Experiment files that were processed by the lab generating the data. |
| lab_processed\/images\/.*
| ✓ | This is a directory containing processed image files |
-| lab_processed\/images\/[^\/]+\.tissue-boundary\.geojson
| | **[QA/QC]** If the boundaries of the tissue have been identified (e.g., by manual efforts), then the boundary geometry can be included as a GeoJSON file named “*.tissue-boundary.geojson”. |
-| lab_processed\/images\/[^\/]+\.ome\.tiff
| ✓ | OME-TIFF file (multichannel, multi-layered) produced by the experiment. If compressed, must use loss-less compression algorithm. See the following link for the set of fields that are required in the OME TIFF file XML header. . It is recommended that you confirm you're using the latest version of Bio-Formats, when generating the OME TIFF, as newer versions have improved XML handling. |
-| lab_processed\/images\/[^\/]*ome-tiff\.channels\.csv
| ✓ | This file provides essential documentation pertaining to each channel of the accommpanying OME TIFF. The file should contain one row per OME TIFF channel. The required fields are detailed |
+| lab_processed\/images\/[^\/]+tissue-boundary\.geojson
| | **[QA/QC]** If the boundaries of the tissue have been identified (e.g., by manual efforts), then the boundary geometry can be included as a GeoJSON file named “*.tissue-boundary.geojson”. |
+| lab_processed\/images\/[^\/]*qptiff\.channels\.csv
| ✓ | This file provides essential documentation pertaining to each channel of the accommpanying QPTIFF. The file should contain one row per QPTIFF channel. The required fields are detailed |
diff --git a/examples/dataset-iec-examples/good-cedar-phenocycler-shared/upload/global/lab_processed/images/OL9.ome.tiff b/examples/dataset-iec-examples/good-cedar-phenocycler-shared/upload/global/lab_processed/images/OL9.ome.tiff
deleted file mode 100644
index e69de29bb..000000000
diff --git a/examples/dataset-iec-examples/good-cedar-phenocycler-shared/upload/global/lab_processed/images/OL9.ome-tiff.channels.csv b/examples/dataset-iec-examples/good-cedar-phenocycler-shared/upload/global/lab_processed/images/OL9.qptiff.channels.csv
similarity index 100%
rename from examples/dataset-iec-examples/good-cedar-phenocycler-shared/upload/global/lab_processed/images/OL9.ome-tiff.channels.csv
rename to examples/dataset-iec-examples/good-cedar-phenocycler-shared/upload/global/lab_processed/images/OL9.qptiff.channels.csv
diff --git a/src/ingest_validation_tools/directory-schemas/phenocycler-v2.yaml b/src/ingest_validation_tools/directory-schemas/phenocycler-v2.yaml
index 94753580a..2101dc8b5 100644
--- a/src/ingest_validation_tools/directory-schemas/phenocycler-v2.yaml
+++ b/src/ingest_validation_tools/directory-schemas/phenocycler-v2.yaml
@@ -60,16 +60,12 @@ files:
required: True
description: This is a directory containing processed image files
-
- pattern: lab_processed\/images\/[^\/]+\.tissue-boundary\.geojson
+ pattern: lab_processed\/images\/[^\/]+tissue-boundary\.geojson
required: False
description: If the boundaries of the tissue have been identified (e.g., by manual efforts), then the boundary geometry can be included as a GeoJSON file named “*.tissue-boundary.geojson”.
is_qa_qc: True
-
- pattern: lab_processed\/images\/[^\/]+\.ome\.tiff
+ pattern: lab_processed\/images\/[^\/]*qptiff\.channels\.csv
required: True
- description: OME-TIFF file (multichannel, multi-layered) produced by the experiment. If compressed, must use loss-less compression algorithm. See the following link for the set of fields that are required in the OME TIFF file XML header. . It is recommended that you confirm you're using the latest version of Bio-Formats, when generating the OME TIFF, as newer versions have improved XML handling.
- is_qa_qc: False
- -
- pattern: lab_processed\/images\/[^\/]*ome-tiff\.channels\.csv
- required: True
- description: This file provides essential documentation pertaining to each channel of the accommpanying OME TIFF. The file should contain one row per OME TIFF channel. The required fields are detailed
+ description: This file provides essential documentation pertaining to each channel of the accommpanying QPTIFF. The file should contain one row per QPTIFF channel. The required fields are detailed
+