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525d246
added in vivo testing facility to list of tag man's groups
jo-mueller Jul 31, 2024
5e1b7df
Added Reconstruction and VAST as tags
jo-mueller Jul 31, 2024
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209 changes: 28 additions & 181 deletions docs/notebooks/synchronize_tags.ipynb
View file
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Original file line number Diff line number Diff line change
Expand Up @@ -17,7 +17,7 @@
},
{
"cell_type": "code",
"execution_count": null,
"execution_count": 1,
"metadata": {},
"outputs": [],
"source": [
Expand All @@ -42,19 +42,19 @@
},
{
"cell_type": "code",
"execution_count": 6,
"execution_count": 29,
"metadata": {},
"outputs": [],
"source": [
"# Replace these with your OMERO server credentials\n",
"OMERO_HOST = 'omero-int.biotec.tu-dresden.de'\n",
"OMERO_PORT = 4064\n",
"OMERO_USER = 'tag-man'\n",
"OMERO_PASS = # add tag-man password here\n",
"OMERO_PASS = 'tagtag'\n",
"OMERO_SECURE = True\n",
"TAG_SET_NAMESPACE = 'openmicroscopy.org/omero/insight/tagset'\n",
"\n",
"TARGET_GROUPS = ['BiAPoL', 'Campas Lab', 'Dye Lab']"
"TARGET_GROUPS = ['BiAPoL', 'Campas Lab', 'Dye Lab', 'In vivo testing facility']"
]
},
{
Expand Down Expand Up @@ -204,177 +204,30 @@
"metadata": {},
"outputs": [
{
"name": "stdout",
"data": {
"text/plain": [
"'in vivo testing facility'"
]
},
"execution_count": 7,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"OMERO_GROUP"
]
},
{
"cell_type": "code",
"execution_count": 30,
"metadata": {},
"outputs": [
{
"name": "stderr",
"output_type": "stream",
"text": [
"Currently connected user's ID: 212\n",
"Tag set 'Biological entity' already exists in OMERO.\n",
"\tTag 'Brain' already exists in tag set 'Biological entity'.\n",
"\tTag 'Cell Culture' already exists in tag set 'Biological entity'.\n",
"\tTag 'Cells' already exists in tag set 'Biological entity'.\n",
"\tTag 'Embryo' already exists in tag set 'Biological entity'.\n",
"\tTag 'Eye' already exists in tag set 'Biological entity'.\n",
"\tTag 'Fin' already exists in tag set 'Biological entity'.\n",
"\tTag 'Gastro-intestinal' already exists in tag set 'Biological entity'.\n",
"\tTag 'Organoid' already exists in tag set 'Biological entity'.\n",
"\tTag 'Spheroid' already exists in tag set 'Biological entity'.\n",
"\tTag 'Tail' already exists in tag set 'Biological entity'.\n",
"\tTag 'Whole organism' already exists in tag set 'Biological entity'.\n",
"\tTag 'Wing Disk' already exists in tag set 'Biological entity'.\n",
"Tag set 'Organism' already exists in OMERO.\n",
"\tTag 'C. elegans' already exists in tag set 'Organism'.\n",
"\tTag 'Drosophila' already exists in tag set 'Organism'.\n",
"\tTag 'Fish' already exists in tag set 'Organism'.\n",
"\tTag 'Human' already exists in tag set 'Organism'.\n",
"\tTag 'Mouse' already exists in tag set 'Organism'.\n",
"\tTag 'Rat' already exists in tag set 'Organism'.\n",
"\tTag 'Zebrafish' already exists in tag set 'Organism'.\n",
"Tag set 'Experimental status' already exists in OMERO.\n",
"\tTag 'Control' already exists in tag set 'Experimental status'.\n",
"\tTag 'Disease' already exists in tag set 'Experimental status'.\n",
"\tTag 'Drug' already exists in tag set 'Experimental status'.\n",
"\tTag 'Mutant' already exists in tag set 'Experimental status'.\n",
"\tTag 'Test' already exists in tag set 'Experimental status'.\n",
"Tag set 'Experimental variable' already exists in OMERO.\n",
"\tTag 'Concentration' already exists in tag set 'Experimental variable'.\n",
"\tTag 'Dose' already exists in tag set 'Experimental variable'.\n",
"\tTag 'Time' already exists in tag set 'Experimental variable'.\n",
"\tTag 'Temperature' already exists in tag set 'Experimental variable'.\n",
"\tTag 'pH' already exists in tag set 'Experimental variable'.\n",
"Tag set 'Extrinsic variable' already exists in OMERO.\n",
"Tag set 'Intrinsic variable' already exists in OMERO.\n",
"\tTag 'Tumor' already exists in tag set 'Intrinsic variable'.\n",
"\tTag 'Wild type' already exists in tag set 'Intrinsic variable'.\n",
"Tag set 'Image data type' already exists in OMERO.\n",
"\tTag 'Raw data' already exists in tag set 'Image data type'.\n",
"\tTag 'Processed' already exists in tag set 'Image data type'.\n",
"\tTag 'Segmentation' already exists in tag set 'Image data type'.\n",
"\tTag 'Stitched' already exists in tag set 'Image data type'.\n",
"\tTag 'Annotation' already exists in tag set 'Image data type'.\n",
"\tTag 'Denoised' already exists in tag set 'Image data type'.\n",
"Tag set 'Imaging method' already exists in OMERO.\n",
"\tTag 'Confocal' already exists in tag set 'Imaging method'.\n",
"\tTag 'Fluorescence' already exists in tag set 'Imaging method'.\n",
"\tTag 'Lightsheet' already exists in tag set 'Imaging method'.\n",
"\tTag 'EM' already exists in tag set 'Imaging method'.\n",
"\tTag 'Widefield' already exists in tag set 'Imaging method'.\n",
"\tTag 'Brightfield' already exists in tag set 'Imaging method'.\n",
"\tTag 'Two-photon' already exists in tag set 'Imaging method'.\n",
"\tTag 'Spinning Disk' already exists in tag set 'Imaging method'.\n",
"\tTag 'Laser Scanning' already exists in tag set 'Imaging method'.\n",
"\tTag 'FLIM' already exists in tag set 'Imaging method'.\n",
"Currently connected user's ID: 212\n",
"Creating tag set 'Biological entity' in OMERO.\n",
"\tCreating tag 'Brain' in tag set 'Biological entity'.\n",
"\tCreating tag 'Cell Culture' in tag set 'Biological entity'.\n",
"\tCreating tag 'Cells' in tag set 'Biological entity'.\n",
"\tCreating tag 'Embryo' in tag set 'Biological entity'.\n",
"\tCreating tag 'Eye' in tag set 'Biological entity'.\n",
"\tCreating tag 'Fin' in tag set 'Biological entity'.\n",
"\tCreating tag 'Gastro-intestinal' in tag set 'Biological entity'.\n",
"\tCreating tag 'Organoid' in tag set 'Biological entity'.\n",
"\tCreating tag 'Spheroid' in tag set 'Biological entity'.\n",
"\tCreating tag 'Tail' in tag set 'Biological entity'.\n",
"\tCreating tag 'Whole organism' in tag set 'Biological entity'.\n",
"\tCreating tag 'Wing Disk' in tag set 'Biological entity'.\n",
"Creating tag set 'Organism' in OMERO.\n",
"\tCreating tag 'C. elegans' in tag set 'Organism'.\n",
"\tCreating tag 'Drosophila' in tag set 'Organism'.\n",
"\tCreating tag 'Fish' in tag set 'Organism'.\n",
"\tCreating tag 'Human' in tag set 'Organism'.\n",
"\tCreating tag 'Mouse' in tag set 'Organism'.\n",
"\tCreating tag 'Rat' in tag set 'Organism'.\n",
"\tCreating tag 'Zebrafish' in tag set 'Organism'.\n",
"Creating tag set 'Experimental status' in OMERO.\n",
"\tCreating tag 'Control' in tag set 'Experimental status'.\n",
"\tCreating tag 'Disease' in tag set 'Experimental status'.\n",
"\tCreating tag 'Drug' in tag set 'Experimental status'.\n",
"\tCreating tag 'Mutant' in tag set 'Experimental status'.\n",
"\tCreating tag 'Test' in tag set 'Experimental status'.\n",
"Creating tag set 'Experimental variable' in OMERO.\n",
"\tCreating tag 'Concentration' in tag set 'Experimental variable'.\n",
"\tCreating tag 'Dose' in tag set 'Experimental variable'.\n",
"\tCreating tag 'Time' in tag set 'Experimental variable'.\n",
"\tCreating tag 'Temperature' in tag set 'Experimental variable'.\n",
"\tCreating tag 'pH' in tag set 'Experimental variable'.\n",
"Creating tag set 'Extrinsic variable' in OMERO.\n",
"Creating tag set 'Intrinsic variable' in OMERO.\n",
"\tCreating tag 'Tumor' in tag set 'Intrinsic variable'.\n",
"\tCreating tag 'Wild type' in tag set 'Intrinsic variable'.\n",
"Creating tag set 'Image data type' in OMERO.\n",
"\tCreating tag 'Raw data' in tag set 'Image data type'.\n",
"\tCreating tag 'Processed' in tag set 'Image data type'.\n",
"\tCreating tag 'Segmentation' in tag set 'Image data type'.\n",
"\tCreating tag 'Stitched' in tag set 'Image data type'.\n",
"\tCreating tag 'Annotation' in tag set 'Image data type'.\n",
"\tCreating tag 'Denoised' in tag set 'Image data type'.\n",
"Creating tag set 'Imaging method' in OMERO.\n",
"\tCreating tag 'Confocal' in tag set 'Imaging method'.\n",
"\tCreating tag 'Fluorescence' in tag set 'Imaging method'.\n",
"\tCreating tag 'Lightsheet' in tag set 'Imaging method'.\n",
"\tCreating tag 'EM' in tag set 'Imaging method'.\n",
"\tCreating tag 'Widefield' in tag set 'Imaging method'.\n",
"\tCreating tag 'Brightfield' in tag set 'Imaging method'.\n",
"\tCreating tag 'Two-photon' in tag set 'Imaging method'.\n",
"\tCreating tag 'Spinning Disk' in tag set 'Imaging method'.\n",
"\tCreating tag 'Laser Scanning' in tag set 'Imaging method'.\n",
"\tCreating tag 'FLIM' in tag set 'Imaging method'.\n",
"Currently connected user's ID: 212\n",
"Creating tag set 'Biological entity' in OMERO.\n",
"\tCreating tag 'Brain' in tag set 'Biological entity'.\n",
"\tCreating tag 'Cell Culture' in tag set 'Biological entity'.\n",
"\tCreating tag 'Cells' in tag set 'Biological entity'.\n",
"\tCreating tag 'Embryo' in tag set 'Biological entity'.\n",
"\tCreating tag 'Eye' in tag set 'Biological entity'.\n",
"\tCreating tag 'Fin' in tag set 'Biological entity'.\n",
"\tCreating tag 'Gastro-intestinal' in tag set 'Biological entity'.\n",
"\tCreating tag 'Organoid' in tag set 'Biological entity'.\n",
"\tCreating tag 'Spheroid' in tag set 'Biological entity'.\n",
"\tCreating tag 'Tail' in tag set 'Biological entity'.\n",
"\tCreating tag 'Whole organism' in tag set 'Biological entity'.\n",
"\tCreating tag 'Wing Disk' in tag set 'Biological entity'.\n",
"Creating tag set 'Organism' in OMERO.\n",
"\tCreating tag 'C. elegans' in tag set 'Organism'.\n",
"\tCreating tag 'Drosophila' in tag set 'Organism'.\n",
"\tCreating tag 'Fish' in tag set 'Organism'.\n",
"\tCreating tag 'Human' in tag set 'Organism'.\n",
"\tCreating tag 'Mouse' in tag set 'Organism'.\n",
"\tCreating tag 'Rat' in tag set 'Organism'.\n",
"\tCreating tag 'Zebrafish' in tag set 'Organism'.\n",
"Creating tag set 'Experimental status' in OMERO.\n",
"\tCreating tag 'Control' in tag set 'Experimental status'.\n",
"\tCreating tag 'Disease' in tag set 'Experimental status'.\n",
"\tCreating tag 'Drug' in tag set 'Experimental status'.\n",
"\tCreating tag 'Mutant' in tag set 'Experimental status'.\n",
"\tCreating tag 'Test' in tag set 'Experimental status'.\n",
"Creating tag set 'Experimental variable' in OMERO.\n",
"\tCreating tag 'Concentration' in tag set 'Experimental variable'.\n",
"\tCreating tag 'Dose' in tag set 'Experimental variable'.\n",
"\tCreating tag 'Time' in tag set 'Experimental variable'.\n",
"\tCreating tag 'Temperature' in tag set 'Experimental variable'.\n",
"\tCreating tag 'pH' in tag set 'Experimental variable'.\n",
"Creating tag set 'Extrinsic variable' in OMERO.\n",
"Creating tag set 'Intrinsic variable' in OMERO.\n",
"\tCreating tag 'Tumor' in tag set 'Intrinsic variable'.\n",
"\tCreating tag 'Wild type' in tag set 'Intrinsic variable'.\n",
"Creating tag set 'Image data type' in OMERO.\n",
"\tCreating tag 'Raw data' in tag set 'Image data type'.\n",
"\tCreating tag 'Processed' in tag set 'Image data type'.\n",
"\tCreating tag 'Segmentation' in tag set 'Image data type'.\n",
"\tCreating tag 'Stitched' in tag set 'Image data type'.\n",
"\tCreating tag 'Annotation' in tag set 'Image data type'.\n",
"\tCreating tag 'Denoised' in tag set 'Image data type'.\n",
"Creating tag set 'Imaging method' in OMERO.\n",
"\tCreating tag 'Confocal' in tag set 'Imaging method'.\n",
"\tCreating tag 'Fluorescence' in tag set 'Imaging method'.\n",
"\tCreating tag 'Lightsheet' in tag set 'Imaging method'.\n",
"\tCreating tag 'EM' in tag set 'Imaging method'.\n",
"\tCreating tag 'Widefield' in tag set 'Imaging method'.\n",
"\tCreating tag 'Brightfield' in tag set 'Imaging method'.\n",
"\tCreating tag 'Two-photon' in tag set 'Imaging method'.\n",
"\tCreating tag 'Spinning Disk' in tag set 'Imaging method'.\n",
"\tCreating tag 'Laser Scanning' in tag set 'Imaging method'.\n",
"\tCreating tag 'FLIM' in tag set 'Imaging method'.\n"
"ERROR:root:Could not connect, check your settings\n"
]
}
],
Expand All @@ -386,16 +239,10 @@
"\n",
"for OMERO_GROUP in TARGET_GROUPS:\n",
" # Connect to OMERO\n",
" conn = ezomero.connect(user=OMERO_USER, password=OMERO_PASS, host=OMERO_HOST, port=OMERO_PORT, secure=True, group=OMERO_GROUP)\n",
" conn = ezomero.connect(user=OMERO_USER, password=OMERO_PASS, host=OMERO_HOST,\n",
" port=OMERO_PORT, secure=OMERO_SECURE, group=OMERO_GROUP)\n",
" synchronize_tags(conn, local_tag_collection)"
]
},
{
"cell_type": "code",
"execution_count": null,
"metadata": {},
"outputs": [],
"source": []
}
],
"metadata": {
Expand Down
6 changes: 5 additions & 1 deletion docs/notebooks/tag_collection.yaml
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -98,6 +98,8 @@ Tagset_image_data_type:
description: ""
- name: "Processed"
description: ""
- name: "Reconstructed"
description: "An image that was reconstructed from several smaller images"
- name: "Segmentation"
description: ""
- name: "Stitched"
Expand Down Expand Up @@ -132,4 +134,6 @@ Tagset_imaging_method:
- name: "FLIM"
description: "Fluorescence lifetime imaging"
- name: "DIC"
description: "Differential interference contrast"
description: "Differential interference contrast"
- name: "VAST"
description: "Vertebrate Automated Screening Technology"