Update "TissueDeformationScaling" field and JSON example

bids-standard · Oct 1, 2021 · 2a5cf25 · 2a5cf25
1 parent b8ad766
commit 2a5cf25
Showing 1 changed file with 3 additions and 3 deletions.
diff --git a/src/04-modality-specific-files/10-microscopy.md b/src/04-modality-specific-files/10-microscopy.md
@@ -261,7 +261,7 @@ It will require changes to `src/schema/metatata/BodyPart.yaml` and `src/04-modal
 | SamplePrimaryAntibody       | RECOMMENDED           | [string][] or [array][] of [strings][] | Description of the primary antibody used for immunostaining. Either an [RRID](https://scicrunch.org/resources) or the name, supplier and catalogue number of a commercial antibody. For non-commercial antibodies either an [RRID](https://scicrunch.org/resources) or the host-animal and immunogen used (for examples: `"RRID:AB_2122563"` or `"Rabbit anti-Human HTR5A Polyclonal Antibody, Invitrogen, Catalog # PA1-2453"`). MAY be an array of strings if different antibodies are used in each channel of the file. |
 | SampleSecondaryAntibody     | RECOMMENDED           | [string][] or [array][] of [strings][] | Description of the secondary antibody used for immunostaining. Either an [RRID](https://scicrunch.org/resources) or the name, supplier and catalogue number of a commercial antibody. For non-commercial antibodies either an [RRID](https://scicrunch.org/resources) or the host-animal and immunogen used (for examples: `"RRID:AB_228322"` or `"Goat anti-Mouse IgM Secondary Antibody, Invitrogen, Catalog # 31172"`). MAY be an array of strings if different antibodies are used in each channel of the file.        |
 | SliceThickness              | OPTIONAL              | [number]                               | Slice thickness of the tissue sample in the unit micrometers (`"um"`) (for example: `5`).                                                                                                                                                                                                                                                                                                                                                                                                                                  |
-| ShrinkageFactor             | OPTIONAL              | [number][]                             | Estimated shrinkage factor of the tissue, given in percent (between 0 and 100%) of the original tissue dimensions (for example: `3`).                                                                                                                                                                                                                                                                                                                                                                                      |
+| TissueDeformationScaling    | OPTIONAL              | [number][]                             | Estimated deformation of the tissue, given as a percentage of the original tissue size (for examples: for a shrinkage of 3%, the value is `97`; and for an expansion of 100%, the value is `200`).                                                                                                                                                                                                                                                                                                                         |
 | SampleExtractionProtocol    | OPTIONAL              | [string][] or [URI][uri]               | Description of the sample extraction protocol or URI from [protocols.io](https://www.protocols.io/).                                                                                                                                                                                                                                                                                                                                                                                                                       |
 | SampleExtractionInstitution | OPTIONAL              | [string][]                             | The name of the institution in charge of the extraction of the sample, if different from the institution in charge of the equipment that produced the image.                                                                                                                                                                                                                                                                                                                                                               |
 
@@ -300,11 +300,11 @@ A "manual" table is provided to facilitate the review process.
         "Magnification": 40,
         "BodyPart": "BRAIN",
         "BodyPartDetails": "corpus callosum",
-        "Environment": "exvivo",
+        "SampleEnvironment": "exvivo",
         "SampleFixation": "4% paraformaldehyde, 2% glutaraldehyde",
         "SampleStaining": "LFB",
         "SliceThickness": 5,
-        "ShrinkageFactor": 3
+        "TissueDeformationScaling": 97
 }
 ```