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Co-authored-by: Chris Markiewicz <[email protected]>
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@mariehbourget @effigies
mariehbourget and effigies authored Oct 1, 2021
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4 changes: 2 additions & 2 deletions src/04-modality-specific-files/10-microscopy.md
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Expand Up @@ -77,7 +77,7 @@ A "manual" table is provided to facilitate the review process.
| --------------------------------------------- | -------- |
| Transmission electron microscopy | TEM |
| Scanning electron microscopy | SEM |
| Micro-CT | CT |
| Micro-CT | uCT |
| Bright-field microscopy | BF |
| Dark-field microscopy | DF |
| Phase-contrast microscopy | PC |
Expand Down Expand Up @@ -254,7 +254,7 @@ It will require changes to `src/schema/metatata/BodyPart.yaml` and `src/04-modal
| BodyPart | RECOMMENDED | [string][] | Body part of the organ / body region scanned. From [DICOM Body Part Examined](http://dicom.nema.org/medical/dicom/current/output/chtml/part16/chapter_L.html#chapter_L) (for example: `"BRAIN"`)". |
| BodyPartDetails | OPTIONAL | [string][] | If needed, additional details about body part or location (for example: `"corpus callosum"`). |
| BodyPartDetailsOntology | OPTIONAL | [string][] | If applicable, information about the ontology used for specifying BodyPartDetails (for example: `"UBERON (https://www.ebi.ac.uk/ols/ontologies/uberon)"`). |
| Environment | RECOMMENDED | [string][] | Indicate if the sample is imaged `"invivo"`, `"exvivo"` or `"invitro"`. |
| SampleEnvironment | RECOMMENDED | [string][] | Indicate if the sample is imaged `"invivo"`, `"exvivo"` or `"invitro"`. |
| SampleEmbedding | OPTIONAL | [string][] | Description of the tissue sample embedding (for example: `"Epoxy resin"`). |
| SampleFixation | OPTIONAL | [string][] | Description of the tissue sample fixation (for example: `"4% paraformaldehyde, 2% glutaraldehyde"`). |
| SampleStaining | RECOMMENDED | [string][] or [array][] of [strings][] | Description of the tissue sample staining (for example: `"Osmium"`). MAY be an array of strings if different stains are used in each channel of the file (for example: `["LFB", "PLP"]`). |
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