diff --git a/.gitattributes b/.gitattributes index 6912e57..33fd528 100644 --- a/.gitattributes +++ b/.gitattributes @@ -1 +1 @@ -yard/data/lfs/*/*.* filter=lfs diff=lfs merge=lfs -text +yard/data/lfs/** filter=lfs diff=lfs merge=lfs -text diff --git a/yard/data/extractors/oscem-life.yml b/yard/data/extractors/oscem-life.yml new file mode 100644 index 0000000..9eaef1c --- /dev/null +++ b/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 }} diff --git a/yard/data/filetypes/epu-dir.yml b/yard/data/filetypes/epu-dir.yml new file mode 100644 index 0000000..be296de --- /dev/null +++ b/yard/data/filetypes/epu-dir.yml @@ -0,0 +1,14 @@ +--- +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 diff --git a/yard/data/filetypes/oscem-json.yml b/yard/data/filetypes/oscem-json.yml new file mode 100644 index 0000000..d2a60c0 --- /dev/null +++ b/yard/data/filetypes/oscem-json.yml @@ -0,0 +1,12 @@ +--- +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 diff --git a/yard/data/filetypes/serialem-dir.yml b/yard/data/filetypes/serialem-dir.yml new file mode 100644 index 0000000..345e19f --- /dev/null +++ b/yard/data/filetypes/serialem-dir.yml @@ -0,0 +1,12 @@ +--- +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 diff --git a/yard/data/lfs/epu-dir/epu_example/FoilHole_31936319_Data_31923985_31923987_20240831_200517.xml b/yard/data/lfs/epu-dir/epu_example/FoilHole_31936319_Data_31923985_31923987_20240831_200517.xml new file mode 100644 index 0000000..93d2e2c --- /dev/null +++ b/yard/data/lfs/epu-dir/epu_example/FoilHole_31936319_Data_31923985_31923987_20240831_200517.xml @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:19933dd0a93c476223cb5dba8a19fe5f184b5f22fcac1f2a7a51f8a2576b5b21 +size 14289 diff --git a/yard/data/lfs/epu-dir/epu_example/FoilHole_31936319_Data_31923988_31923990_20240831_200519.xml b/yard/data/lfs/epu-dir/epu_example/FoilHole_31936319_Data_31923988_31923990_20240831_200519.xml new file mode 100644 index 0000000..71c9928 --- /dev/null +++ b/yard/data/lfs/epu-dir/epu_example/FoilHole_31936319_Data_31923988_31923990_20240831_200519.xml @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:ea5d102590f4241bdfe67bb0178685a8565e29c16405769fd4ed3b05c80d46c4 +size 14292 diff --git a/yard/data/lfs/epu-dir/epu_example/FoilHole_31936319_Data_31923991_31923993_20240831_200522.xml b/yard/data/lfs/epu-dir/epu_example/FoilHole_31936319_Data_31923991_31923993_20240831_200522.xml new file mode 100644 index 0000000..8f5f112 --- /dev/null +++ b/yard/data/lfs/epu-dir/epu_example/FoilHole_31936319_Data_31923991_31923993_20240831_200522.xml @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:9f62559f8bb4cc20c8941d4b485e0ccd61ab3e7f1f6adc78e71a84ccdbac7f8a +size 14290 diff --git a/yard/data/lfs/epu-dir/epu_example/FoilHole_31936319_Data_31923994_31923996_20240831_200524.xml b/yard/data/lfs/epu-dir/epu_example/FoilHole_31936319_Data_31923994_31923996_20240831_200524.xml new file mode 100644 index 0000000..cb52cf3 --- /dev/null +++ b/yard/data/lfs/epu-dir/epu_example/FoilHole_31936319_Data_31923994_31923996_20240831_200524.xml @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:05a150380c6174f54b597d406c66b32ee3eb5c1d2068738a2e4207cbd3e155be +size 14291 diff --git a/yard/data/lfs/epu-dir/epu_example/FoilHole_31936319_Data_31923997_31923999_20240831_200529.xml b/yard/data/lfs/epu-dir/epu_example/FoilHole_31936319_Data_31923997_31923999_20240831_200529.xml new file mode 100644 index 0000000..3c0f331 --- /dev/null +++ b/yard/data/lfs/epu-dir/epu_example/FoilHole_31936319_Data_31923997_31923999_20240831_200529.xml @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:0ad251b98debfbe385155c7d2e547d972884dfc637e2c474ff32f5fd86531405 +size 14291 diff --git a/yard/data/lfs/epu-dir/epu_example/FoilHole_31936319_Data_31924000_31924003_20240831_200533.xml b/yard/data/lfs/epu-dir/epu_example/FoilHole_31936319_Data_31924000_31924003_20240831_200533.xml new file mode 100644 index 0000000..16420ef --- /dev/null +++ b/yard/data/lfs/epu-dir/epu_example/FoilHole_31936319_Data_31924000_31924003_20240831_200533.xml @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:d7f1e5ac33f9b73316ebb5a9b0ffc7e163db92e4c1c0475fe59aac0e30644870 +size 14290 diff --git a/yard/data/lfs/epu-dir/epu_example/FoilHole_31936319_Data_31924004_31924006_20240831_200538.xml b/yard/data/lfs/epu-dir/epu_example/FoilHole_31936319_Data_31924004_31924006_20240831_200538.xml new file mode 100644 index 0000000..d392ef0 --- /dev/null +++ b/yard/data/lfs/epu-dir/epu_example/FoilHole_31936319_Data_31924004_31924006_20240831_200538.xml @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:b95475755b40e0963318b9e63b9b01c933b0948aeaf1c24c47a895954334a7e3 +size 14292 diff --git a/yard/data/lfs/epu-dir/epu_example/FoilHole_31936319_Data_31924007_31924009_20240831_200542.xml b/yard/data/lfs/epu-dir/epu_example/FoilHole_31936319_Data_31924007_31924009_20240831_200542.xml new file mode 100644 index 0000000..41c69e0 --- /dev/null +++ b/yard/data/lfs/epu-dir/epu_example/FoilHole_31936319_Data_31924007_31924009_20240831_200542.xml @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:65891851b769541a559cfa24229e7f09c72f99daa10513d15fe30d1ac1cedf41 +size 14291 diff --git a/yard/data/lfs/epu-dir/epu_example/FoilHole_31936319_Data_31924010_31924012_20240831_200547.xml b/yard/data/lfs/epu-dir/epu_example/FoilHole_31936319_Data_31924010_31924012_20240831_200547.xml new file mode 100644 index 0000000..690cc10 --- /dev/null +++ b/yard/data/lfs/epu-dir/epu_example/FoilHole_31936319_Data_31924010_31924012_20240831_200547.xml @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:53a1671c3676c280787538b05df06a43fcb57884f008a3505357f69a00a60dbf +size 14290 diff --git a/yard/data/lfs/epu-dir/epu_example/FoilHole_31936319_Data_31924013_31924015_20240831_200551.xml b/yard/data/lfs/epu-dir/epu_example/FoilHole_31936319_Data_31924013_31924015_20240831_200551.xml new file mode 100644 index 0000000..337110b --- /dev/null +++ b/yard/data/lfs/epu-dir/epu_example/FoilHole_31936319_Data_31924013_31924015_20240831_200551.xml @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:6689f86ce9e8254ccacf2eb3bdde58ef818d0ac9d6d5c3932127a2fd8ca708f5 +size 14292