diff --git a/episodes/fig/metadata-console.png b/episodes/fig/metadata-console.png index d612ab32..34fc3b9c 100644 Binary files a/episodes/fig/metadata-console.png and b/episodes/fig/metadata-console.png differ diff --git a/episodes/filetypes-and-metadata.md b/episodes/filetypes-and-metadata.md index 271cf409..1ba25f9d 100644 --- a/episodes/filetypes-and-metadata.md +++ b/episodes/filetypes-and-metadata.md @@ -141,13 +141,24 @@ print(metadata) ``` ```output OME( - experimenters=[{'id': 'Experimenter:0', 'user_name': 'Zeiss'}], - instruments=[<1 field_type>], - images=[<1 field_type>], + plates=[<1 field_type>], + experimenters=[{'id': 'Experimenter:Zeiss', 'user_name': 'Zeiss'}], + instruments=[<1 field_type>], + images=[<2 field_type>], + structured_annotations={ + 'xml_annotations': [ + { + 'description': 'ZEN 2012 (blue edition)1.1.1.0', + 'id': 'urn:lsid:allencell.org:Annotation:AcquisitionSoftware', + 'value': {}, + 'kind': 'xmlannotation' + } + ] + } ) ``` -In this case, we can see it is split into three categories: +In this case, we can see it is split into various categories including `experimenters`, `images` and `instruments`. You can look inside each of these using `.category` e.g.: ```python @@ -174,7 +185,7 @@ processing steps don't overwrite this original image. Explore the metadata in the console to answer the following questions: -- What type of microscope was used to take this image? +- Which manufacturer made the microscope used to take this image? - What detector was used to take this image? - What does each channel show? For example, which fluorophore is used? What is its excitation and emission wavelength? (hint: look inside the image's @@ -184,10 +195,10 @@ pixel metadata: `metadata.images[0].pixels`) ## Solution -### Microscope model +### Microscope manufacturer -Under `metadata.instruments[0].microscope`, we can see that an 'Axio Imager Z2' -microscope was used. +Under `metadata.instruments[0].microscope`, we can see that the microscope +manufacturer was Zeiss. ### Detector Under `metadata.instruments[0].detectors`, we can see @@ -196,18 +207,18 @@ that this used an HDCamC10600-30B (ORCA-R2) detector. ### Channels Under `metadata.images[0].pixels.channels`, we can see one entry per channel -- `Channel:0:0`, `Channel:0:1` and `Channel:0:2`. +- `Channel:1:0`, `Channel:2:0` and `Channel:3:0`. In the first (`metadata.images[0].pixels.channels[0]`), we can see that its -`name` is TagYFP, a fluorophore with `emission_wavelength` of 524nm and +`fluor` is TagYFP, a fluorophore with `emission_wavelength` of 524nm and `excitation_wavelength` of 508nm. -In the first (`metadata.images[0].pixels.channels[1]`), we can see that its -`name` is mRFP1.2, a fluorophore with `emission_wavelength` of 612nm and +In the second (`metadata.images[0].pixels.channels[1]`), we can see that its +`fluor` is mRFP1.2, a fluorophore with `emission_wavelength` of 612nm and `excitation_wavelength` of 590nm. -In the first (`metadata.images[0].pixels.channels[2]`), we see that its name -is `TL DIC` and no `emission_wavelength` or `excitation_wavelength` is listed. +In the last (`metadata.images[0].pixels.channels[2]`), we see that no `fluor`, +`emission_wavelength` or `excitation_wavelength` is listed. Its `illumination_type` is listed as 'transmitted', so this is simply an image of the yeast cells with no fluorophores used.