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Merged
jburel merged 4 commits into from
Jun 29, 2026
Merged

No idr #65

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8ee4e5c
Fix the idr0021 notebook to point to workshop
pwalczysko Jun 25, 2026
6c401f2
Bump omero-py
pwalczysko Jun 25, 2026
04ea374
Redirect idr0062_prediction to idr0062_prediction_save
pwalczysko Jun 25, 2026
301fc0a
Fix the ice-python wheel and the omero-py vers in the ...62_pred.._save
pwalczysko Jun 25, 2026
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30 changes: 17 additions & 13 deletions notebooks/idr0021_segmentation.ipynb
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Original file line number Diff line number Diff line change
Expand Up @@ -9,7 +9,7 @@
"\n",
"[![Open in Colab](https://colab.research.google.com/assets/colab-badge.svg)](https://colab.research.google.com/github/ome/omero-guide-python/blob/master/notebooks/idr0021_segmentation.ipynb)\n",
"\n",
"This notebook uses the idr0021 dataset [idr0021-lawo-pericentriolarmaterial/experimentA](https://idr.openmicroscopy.org/webclient/?show=project-51) and tries to reproduce some of the analysis published in ['Subdiffraction imaging of centrosomes reveals higher-order organizational features of pericentriolar material']((https://doi.org/10.1038/ncb2591); in particular to create a figure similar to [Figure 1](https://www.nature.com/articles/ncb2591/figures/1) of the article."
"This notebook uses the idr0021 dataset [idr0021-lawo-pericentriolarmaterial/experimentA](https://idr.openmicroscopy.org/webclient/?show=project-51) loaded onto an OMERO server and tries to reproduce some of the analysis published in ['Subdiffraction imaging of centrosomes reveals higher-order organizational features of pericentriolar material']((https://doi.org/10.1038/ncb2591); in particular to create a figure similar to [Figure 1](https://www.nature.com/articles/ncb2591/figures/1) of the article."
]
},
{
Expand All @@ -23,15 +23,15 @@
},
{
"cell_type": "code",
"execution_count": 2,
"execution_count": null,
"id": "official-worthy",
"metadata": {},
"outputs": [],
"source": [
"# Ice Python binding\n",
"%pip install https://github.com/glencoesoftware/zeroc-ice-py-linux-x86_64/releases/download/20240202/zeroc_ice-3.6.5-cp310-cp310-manylinux_2_28_x86_64.whl\n",
"%pip install https://github.com/glencoesoftware/zeroc-ice-py-linux-x86_64/releases/download/20240202/zeroc_ice-3.6.5-cp312-cp312-manylinux_2_28_x86_64.whl\n",
"# Package required to interact with IDR or OMERO\n",
"%pip install omero-py==5.19.2"
"%pip install omero-py==5.22.1"
]
},
{
Expand Down Expand Up @@ -59,12 +59,12 @@
"id": "welcome-argument",
"metadata": {},
"source": [
"### Create a connection to IDR"
"### Create a connection to OMERO"
]
},
{
"cell_type": "code",
"execution_count": 3,
"execution_count": null,
"id": "electoral-kitchen",
"metadata": {},
"outputs": [
Expand All @@ -77,29 +77,33 @@
}
],
"source": [
"HOST = 'ws://idr.openmicroscopy.org/omero-ws'\n",
"conn = BlitzGateway('public', 'public',\n",
"from omero.gateway import BlitzGateway\n",
"\n",
"from getpass import getpass\n",
"\n",
"HOST = 'wss://workshop.openmicroscopy.org/omero-ws'\n",
"conn = BlitzGateway(input(\"Username: \"),\n",
" getpass(\"OMERO Password: \"),\n",
" host=HOST, secure=True)\n",
"print(conn.connect())\n",
"conn.c.enableKeepAlive(60)"
"conn.connect()"
]
},
{
"cell_type": "markdown",
"id": "joined-badge",
"metadata": {},
"source": [
"### IDR image to analyze"
"### Image to analyze"
]
},
{
"cell_type": "code",
"execution_count": 4,
"execution_count": null,
"id": "eleven-hamburg",
"metadata": {},
"outputs": [],
"source": [
"image_id = 1884839"
"image_id = 9571"
]
},
{
Expand Down
483 changes: 3 additions & 480 deletions notebooks/idr0062_prediction.ipynb
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6 changes: 3 additions & 3 deletions notebooks/idr0062_prediction_save.ipynb
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Original file line number Diff line number Diff line change
Expand Up @@ -36,15 +36,15 @@
},
{
"cell_type": "code",
"execution_count": 38,
"execution_count": null,
"id": "hydraulic-security",
"metadata": {},
"outputs": [],
"source": [
"# Ice Python binding\n",
"%pip install https://github.com/glencoesoftware/zeroc-ice-py-linux-x86_64/releases/download/20240202/zeroc_ice-3.6.5-cp311-cp311-manylinux_2_28_x86_64.whl\n",
"%pip install https://github.com/glencoesoftware/zeroc-ice-py-linux-x86_64/releases/download/20240202/zeroc_ice-3.6.5-cp312-cp312-manylinux_2_28_x86_64.whl\n",
"# Package required to interact with IDR or OMERO\n",
"%pip install omero-py==5.21.0\n",
"%pip install omero-py==5.22.1\n",
"%pip install cellpose==3.1.1.2"
]
},
Expand Down
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