Updating canonical tomogram selection for gjensen (#22)

chanzuckerberg · Mar 6, 2024 · 0d6c5fd · 0d6c5fd
1 parent c2fc3fb
commit 0d6c5fd
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Showing 62 changed files with 1,141 additions and 1,147 deletions.
diff --git a/ingestion_tools/dataset_configs/gjensen/10054.yaml b/ingestion_tools/dataset_configs/gjensen/10054.yaml
@@ -89,7 +89,7 @@ tomograms:
   reconstruction_method: '{tomo-reconstruction_method}'
   reconstruction_software: '{tomo-reconstruction_software}'
   tomogram_version: 1
-  voxel_spacing: 16.145
+  voxel_spacing: '{tomo-voxel_spacing}'
 annotations: {}
 standardization_config:
   destination_prefix: '10054'

diff --git a/ingestion_tools/dataset_configs/gjensen/10105.yaml b/ingestion_tools/dataset_configs/gjensen/10105.yaml
@@ -86,7 +86,7 @@ tomograms:
     z: 0
   processing: raw
   processing_software: '{tomo-processing_software}'
-  reconstruction_method: '{tomo-reconstruction_method}'
+  reconstruction_method: Weighted back projection
   reconstruction_software: IMOD
   tomogram_version: 1
   voxel_spacing: '{tomo-voxel_spacing}'

diff --git a/ingestion_tools/dataset_configs/gjensen/10108.yaml b/ingestion_tools/dataset_configs/gjensen/10108.yaml
@@ -86,7 +86,7 @@ tomograms:
     z: 0
   processing: raw
   processing_software: IMOD
-  reconstruction_method: '{tomo-reconstruction_method}'
+  reconstruction_method: Weighted back projection
   reconstruction_software: IMOD
   tomogram_version: 1
   voxel_spacing: '{tomo-voxel_spacing}'

diff --git a/ingestion_tools/dataset_configs/gjensen/10145.yaml b/ingestion_tools/dataset_configs/gjensen/10145.yaml
@@ -58,6 +58,19 @@ tiltseries:
   tilting_scheme: starting tilt to max then min
   total_flux: 160.0
 tomograms:
+  voxel_spacing: 16.145
+  reconstruction_method: Weighted back projection
+  reconstruction_software: IMOD
+  fiducial_alignment_status: FIDUCIAL
+  ctf_corrected: null
+  processing: raw
+  processing_software: null
+  align_softwares:
+  - RAPTOR
+  offset:
+    x: 0
+    y: 0
+    z: 0
   affine_transformation_matrix:
   - - 1
     - 0
@@ -75,21 +88,8 @@ tomograms:
     - 0
     - 0
     - 1
-  align_softwares:
-  - RAPTOR
   authors: *id001
-  ctf_corrected: null
-  fiducial_alignment_status: FIDUCIAL
-  offset:
-    x: 0
-    y: 0
-    z: 0
-  processing: raw
-  processing_software: null
-  reconstruction_method: '{tomo-reconstruction_method}'
-  reconstruction_software: IMOD
   tomogram_version: 1
-  voxel_spacing: '{tomo-voxel_spacing}'
 annotations: {}
 standardization_config:
   destination_prefix: '10145'

diff --git a/ingestion_tools/dataset_configs/gjensen/10176.yaml b/ingestion_tools/dataset_configs/gjensen/10176.yaml
@@ -64,6 +64,19 @@ tiltseries:
   tilting_scheme: min to max tilt
   total_flux: 150.0
 tomograms:
+  voxel_spacing: 18.919999999999998
+  reconstruction_method: Weighted back projection
+  reconstruction_software: IMOD
+  fiducial_alignment_status: FIDUCIAL
+  ctf_corrected: null
+  processing: raw
+  processing_software: null
+  align_softwares:
+  - IMOD
+  offset:
+    x: 0
+    y: 0
+    z: 0
   affine_transformation_matrix:
   - - 1
     - 0
@@ -81,21 +94,8 @@ tomograms:
     - 0
     - 0
     - 1
-  align_softwares:
-  - IMOD
   authors: *id001
-  ctf_corrected: null
-  fiducial_alignment_status: FIDUCIAL
-  offset:
-    x: 0
-    y: 0
-    z: 0
-  processing: raw
-  processing_software: null
-  reconstruction_method: '{tomo-reconstruction_method}'
-  reconstruction_software: IMOD
   tomogram_version: 1
-  voxel_spacing: 18.919999999999998
 annotations: {}
 standardization_config:
   destination_prefix: '10176'

diff --git a/ingestion_tools/dataset_configs/gjensen/10209.yaml b/ingestion_tools/dataset_configs/gjensen/10209.yaml
@@ -44,7 +44,7 @@ tiltseries:
     energy_filter: GIF
     image_corrector: null
     phase_plate: false
-  pixel_spacing: 7.8
+  pixel_spacing: 7.800000000000001
   spherical_aberration_constant: 2.0
   tilt_alignment_software: RAPTOR
   tilt_axis: 0.0
@@ -57,7 +57,7 @@ tiltseries:
   tilting_scheme: starting tilt to max then min
   total_flux: 200.0
 tomograms:
-  voxel_spacing: 7.8
+  voxel_spacing: 7.800000000000001
   reconstruction_method: Weighted back projection
   reconstruction_software: IMOD
   fiducial_alignment_status: FIDUCIAL

diff --git a/ingestion_tools/dataset_configs/gjensen/10248.yaml b/ingestion_tools/dataset_configs/gjensen/10248.yaml
@@ -58,19 +58,6 @@ tiltseries:
   tilting_scheme: starting tilt to max then min
   total_flux: 200.0
 tomograms:
-  voxel_spacing: 18.919999999999998
-  reconstruction_method: Weighted back projection
-  reconstruction_software: IMOD
-  fiducial_alignment_status: FIDUCIAL
-  ctf_corrected: null
-  processing: raw
-  processing_software: null
-  align_softwares:
-  - RAPTOR
-  offset:
-    x: 0
-    y: 0
-    z: 0
   affine_transformation_matrix:
   - - 1
     - 0
@@ -88,8 +75,21 @@ tomograms:
     - 0
     - 0
     - 1
+  align_softwares:
+  - RAPTOR
   authors: *id001
+  ctf_corrected: null
+  fiducial_alignment_status: FIDUCIAL
+  offset:
+    x: 0
+    y: 0
+    z: 0
+  processing: raw
+  processing_software: null
+  reconstruction_method: '{tomo-reconstruction_method}'
+  reconstruction_software: IMOD
   tomogram_version: 1
+  voxel_spacing: '{tomo-voxel_spacing}'
 annotations: {}
 standardization_config:
   destination_prefix: '10248'

diff --git a/ingestion_tools/dataset_configs/gjensen/10261.yaml b/ingestion_tools/dataset_configs/gjensen/10261.yaml
@@ -88,7 +88,7 @@ tomograms:
   reconstruction_method: '{tomo-reconstruction_method}'
   reconstruction_software: IMOD
   tomogram_version: 1
-  voxel_spacing: '{tomo-voxel_spacing}'
+  voxel_spacing: 16.145
 annotations: {}
 standardization_config:
   destination_prefix: '10261'

diff --git a/ingestion_tools/dataset_configs/gjensen/10268.yaml b/ingestion_tools/dataset_configs/gjensen/10268.yaml
@@ -86,10 +86,10 @@ tomograms:
     z: 0
   processing: raw
   processing_software: null
-  reconstruction_method: '{tomo-reconstruction_method}'
+  reconstruction_method: Weighted back projection
   reconstruction_software: IMOD
   tomogram_version: 1
-  voxel_spacing: '{tomo-voxel_spacing}'
+  voxel_spacing: 13.059000000000001
 annotations: {}
 standardization_config:
   destination_prefix: '10268'

diff --git a/ingestion_tools/dataset_configs/gjensen/10276.yaml b/ingestion_tools/dataset_configs/gjensen/10276.yaml
@@ -89,7 +89,7 @@ tomograms:
   reconstruction_method: Weighted back projection
   reconstruction_software: IMOD
   tomogram_version: 1
-  voxel_spacing: '{tomo-voxel_spacing}'
+  voxel_spacing: 13.059000000000001
 annotations: {}
 standardization_config:
   destination_prefix: '10276'

diff --git a/ingestion_tools/dataset_configs/gjensen/10289.yaml b/ingestion_tools/dataset_configs/gjensen/10289.yaml
@@ -58,6 +58,19 @@ tiltseries:
   tilting_scheme: starting tilt to max then min
   total_flux: 150.0
 tomograms:
+  voxel_spacing: 15.64
+  reconstruction_method: Weighted back projection
+  reconstruction_software: IMOD
+  fiducial_alignment_status: FIDUCIAL
+  ctf_corrected: null
+  processing: raw
+  processing_software: null
+  align_softwares:
+  - RAPTOR
+  offset:
+    x: 0
+    y: 0
+    z: 0
   affine_transformation_matrix:
   - - 1
     - 0
@@ -75,21 +88,8 @@ tomograms:
     - 0
     - 0
     - 1
-  align_softwares:
-  - RAPTOR
   authors: *id001
-  ctf_corrected: null
-  fiducial_alignment_status: FIDUCIAL
-  offset:
-    x: 0
-    y: 0
-    z: 0
-  processing: raw
-  processing_software: null
-  reconstruction_method: '{tomo-reconstruction_method}'
-  reconstruction_software: IMOD
   tomogram_version: 1
-  voxel_spacing: 15.64
 annotations: {}
 standardization_config:
   destination_prefix: '10289'

diff --git a/ingestion_tools/dataset_configs/gjensen/10290.yaml b/ingestion_tools/dataset_configs/gjensen/10290.yaml
@@ -58,6 +58,19 @@ tiltseries:
   tilting_scheme: starting tilt to max then min
   total_flux: 150.0
 tomograms:
+  voxel_spacing: 15.64
+  reconstruction_method: Weighted back projection
+  reconstruction_software: IMOD
+  fiducial_alignment_status: FIDUCIAL
+  ctf_corrected: null
+  processing: raw
+  processing_software: null
+  align_softwares:
+  - RAPTOR
+  offset:
+    x: 0
+    y: 0
+    z: 0
   affine_transformation_matrix:
   - - 1
     - 0
@@ -75,21 +88,8 @@ tomograms:
     - 0
     - 0
     - 1
-  align_softwares:
-  - RAPTOR
   authors: *id001
-  ctf_corrected: null
-  fiducial_alignment_status: FIDUCIAL
-  offset:
-    x: 0
-    y: 0
-    z: 0
-  processing: raw
-  processing_software: null
-  reconstruction_method: '{tomo-reconstruction_method}'
-  reconstruction_software: IMOD
   tomogram_version: 1
-  voxel_spacing: '{tomo-voxel_spacing}'
 annotations: {}
 standardization_config:
   destination_prefix: '10290'

diff --git a/ingestion_tools/dataset_configs/gjensen/10291.yaml b/ingestion_tools/dataset_configs/gjensen/10291.yaml
@@ -58,6 +58,19 @@ tiltseries:
   tilting_scheme: starting tilt to max then min
   total_flux: 180.0
 tomograms:
+  voxel_spacing: 15.64
+  reconstruction_method: Weighted back projection
+  reconstruction_software: IMOD
+  fiducial_alignment_status: FIDUCIAL
+  ctf_corrected: null
+  processing: raw
+  processing_software: null
+  align_softwares:
+  - RAPTOR
+  offset:
+    x: 0
+    y: 0
+    z: 0
   affine_transformation_matrix:
   - - 1
     - 0
@@ -75,21 +88,8 @@ tomograms:
     - 0
     - 0
     - 1
-  align_softwares:
-  - RAPTOR
   authors: *id001
-  ctf_corrected: null
-  fiducial_alignment_status: FIDUCIAL
-  offset:
-    x: 0
-    y: 0
-    z: 0
-  processing: raw
-  processing_software: null
-  reconstruction_method: '{tomo-reconstruction_method}'
-  reconstruction_software: IMOD
   tomogram_version: 1
-  voxel_spacing: '{tomo-voxel_spacing}'
 annotations: {}
 standardization_config:
   destination_prefix: '10291'

diff --git a/ingestion_tools/dataset_configs/gjensen/10292.yaml b/ingestion_tools/dataset_configs/gjensen/10292.yaml
@@ -58,6 +58,19 @@ tiltseries:
   tilting_scheme: starting tilt to max then min
   total_flux: 150.0
 tomograms:
+  voxel_spacing: 15.64
+  reconstruction_method: Weighted back projection
+  reconstruction_software: IMOD
+  fiducial_alignment_status: FIDUCIAL
+  ctf_corrected: null
+  processing: raw
+  processing_software: null
+  align_softwares:
+  - RAPTOR
+  offset:
+    x: 0
+    y: 0
+    z: 0
   affine_transformation_matrix:
   - - 1
     - 0
@@ -75,21 +88,8 @@ tomograms:
     - 0
     - 0
     - 1
-  align_softwares:
-  - RAPTOR
   authors: *id001
-  ctf_corrected: null
-  fiducial_alignment_status: FIDUCIAL
-  offset:
-    x: 0
-    y: 0
-    z: 0
-  processing: raw
-  processing_software: null
-  reconstruction_method: '{tomo-reconstruction_method}'
-  reconstruction_software: IMOD
   tomogram_version: 1
-  voxel_spacing: 15.64
 annotations: {}
 standardization_config:
   destination_prefix: '10292'

diff --git a/ingestion_tools/dataset_configs/gjensen/10296.yaml b/ingestion_tools/dataset_configs/gjensen/10296.yaml
@@ -85,7 +85,7 @@ tomograms:
     z: 0
   processing: raw
   processing_software: null
-  reconstruction_method: '{tomo-reconstruction_method}'
+  reconstruction_method: Weighted back projection
   reconstruction_software: IMOD
   tomogram_version: 1
   voxel_spacing: '{tomo-voxel_spacing}'

diff --git a/ingestion_tools/dataset_configs/gjensen/10297.yaml b/ingestion_tools/dataset_configs/gjensen/10297.yaml
@@ -85,7 +85,7 @@ tomograms:
     z: 0
   processing: raw
   processing_software: null
-  reconstruction_method: '{tomo-reconstruction_method}'
+  reconstruction_method: Weighted back projection
   reconstruction_software: IMOD
   tomogram_version: 1
   voxel_spacing: '{tomo-voxel_spacing}'