diff --git a/docs/notebooks/synchronize_tags.ipynb b/docs/notebooks/synchronize_tags.ipynb index 44d6a34..166e1ee 100644 --- a/docs/notebooks/synchronize_tags.ipynb +++ b/docs/notebooks/synchronize_tags.ipynb @@ -17,7 +17,7 @@ }, { "cell_type": "code", - "execution_count": null, + "execution_count": 1, "metadata": {}, "outputs": [], "source": [ @@ -42,7 +42,7 @@ }, { "cell_type": "code", - "execution_count": 6, + "execution_count": 29, "metadata": {}, "outputs": [], "source": [ @@ -50,11 +50,11 @@ "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']" ] }, { @@ -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" ] } ], @@ -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": { diff --git a/docs/notebooks/tag_collection.yaml b/docs/notebooks/tag_collection.yaml index a7ee116..a1c3bb6 100644 --- a/docs/notebooks/tag_collection.yaml +++ b/docs/notebooks/tag_collection.yaml @@ -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" @@ -132,4 +134,6 @@ Tagset_imaging_method: - name: "FLIM" description: "Fluorescence lifetime imaging" - name: "DIC" - description: "Differential interference contrast" \ No newline at end of file + description: "Differential interference contrast" + - name: "VAST" + description: "Vertebrate Automated Screening Technology" \ No newline at end of file