Add oscem-life extractor

.gitattributes

@@ -1 +1 @@
-yard/data/lfs/*/*.* filter=lfs diff=lfs merge=lfs -text
+yard/data/lfs/** filter=lfs diff=lfs merge=lfs -text

yard/data/extractors/oscem-life.yml

@@ -0,0 +1,27 @@
+---
+id: >-
+    oscem-life
+name: >-
+    OSC-EM Life Sciences Extractor
+description: >-
+    Extract metadata from electron microscopes for life science applications.
+
+    Reads project directories from SerialEM, EPU, and TOMO5. Outputs the Open Science
+    Community for Electron Microscopy (OSC-EM) standards (single particle analysis, or
+    tomography).
+supported_filetypes:
+    - id: serialem-dir
+    - id: epu-dir
+supported_output_filetypes:
+    - id: oscem-json
+license:
+    spdx: BSD-3-Clause
+subject:
+    - electron-microscopy
+    - imaging
+source_repository: https://github.com/SwissOpenEM/LS_Metadata_reader/
+documentation: https://github.com/SwissOpenEM/LS_Metadata_reader
+usage:
+    - method: container
+      setup: ghcr.io/swissopenem/ls_metadata_reader:main
+      command: -o {{output_path}} {{ input_path }}

yard/data/filetypes/epu-dir.yml

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+---
+id: >-
+    epu-dir
+name: >-
+    Thermo Fisher EPU Project directory
+description: >-
+    Represents a project directory created by Thermo Fisher Scientific's EPU. It should
+    include metadata xml files.
+subject:
+    - electron-microscopy
+associated_software:
+    - EPU
+associated_vendors:
+    - Thermo Fisher Scientific

yard/data/filetypes/oscem-json.yml

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+---
+id: >-
+    oscem-json
+name: >-
+    Electron microscopy metadata following the Open Science Community for Electron
+    Microscopy (OSC-EM) standards.
+description: >-
+    A format for Fischer Scope Indenter
+associated_file_extensions:
+    - json
+subject:
+    - electron-microscopy

yard/data/filetypes/serialem-dir.yml

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+---
+id: >-
+    serialem-dir
+name: >-
+    SerialEM Project directory
+description: >-
+    Represents a project directory created by the SerialEM software for electron
+    microscopy data acquisition.
+subject:
+    - electron-microscopy
+associated_software:
+    - SerialEM