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Cite TSAI in tiling notebooks, deprecating them #420

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merged 5 commits into from
Sep 14, 2023
Merged

Cite TSAI in tiling notebooks, deprecating them #420

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4a37501
Add paper citations for Albert's tiler
alex-l-kong Sep 7, 2023
c7cccc6
Merge branch 'main' into deprecate_tiler
alex-l-kong Sep 7, 2023
5f0a642
Update 2_create_tiled_mibi_run.ipynb
ag-tsai Sep 12, 2023
939f4b5
Update 2_create_tma_mibi_run.ipynb
ag-tsai Sep 12, 2023
97f5cb7
Merge branch 'main' into deprecate_tiler
alex-l-kong Sep 14, 2023
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16 changes: 15 additions & 1 deletion templates/2_create_tiled_mibi_run.ipynb
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Original file line number Diff line number Diff line change
Expand Up @@ -7,6 +7,13 @@
"# Generate tiled region run file"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"## NOTE: the functionality of this notebook has been ported over to TSAI (https://tsai.stanford.edu/research/mibi_tsai). $^1$"
]
},
{
"cell_type": "markdown",
"metadata": {},
Expand Down Expand Up @@ -190,6 +197,13 @@
"\n",
"json_utils.split_run_file(tiled_regions_dir, os.path.basename(tiled_region_path), file_split)"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"$^1$ Piyadasa H, Oberlton B, and Kong A, et al. (2023). Rapid Setup of Tissue Microarray and Tiled Area Imaging on the Multiplexed Ion Beam Imaging Microscope using the Tile/SED/Array Interface. <i>J Vis Exp</i>, [OnlineFirst], https://www.jove.com/t/65615/rapid-setup-tissue-microarray-tiled-area-imaging-on-multiplexed-ion"
]
}
],
"metadata": {
Expand All @@ -208,7 +222,7 @@
"name": "python",
"nbconvert_exporter": "python",
"pygments_lexer": "ipython3",
"version": "3.8.13"
"version": "3.8.15"
}
},
"nbformat": 4,
Expand Down
20 changes: 18 additions & 2 deletions templates/2_create_tma_mibi_run.ipynb
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Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -8,6 +8,14 @@
"# Autolabel TMA Cores"
]
},
{
"cell_type": "markdown",
"id": "c5b74a05-4bbb-447b-ba20-1973149b6303",
"metadata": {},
"source": [
"## NOTE: the functionality of this notebook has been ported over to TSAI (https://tsai.stanford.edu/research/mibi_tsai). $^1$"
]
},
{
"cell_type": "markdown",
"id": "77e6afe1",
Expand Down Expand Up @@ -387,11 +395,19 @@
"\n",
"json_utils.split_run_file(tma_dir, os.path.basename(remapped_fov_path), file_split)"
]
},
{
"cell_type": "markdown",
"id": "0cd7340c-b7d6-4f54-a8cf-2ee2e1faccb3",
"metadata": {},
"source": [
"$^1$ Piyadasa H, Oberlton B, and Kong A, et al. (2023). Rapid Setup of Tissue Microarray and Tiled Area Imaging on the Multiplexed Ion Beam Imaging Microscope using the Tile/SED/Array Interface. <i>J Vis Exp</i>, [OnlineFirst], https://www.jove.com/t/65615/rapid-setup-tissue-microarray-tiled-area-imaging-on-multiplexed-ion"
]
}
],
"metadata": {
"kernelspec": {
"display_name": "Python 3",
"display_name": "Python 3 (ipykernel)",
"language": "python",
"name": "python3"
},
Expand All @@ -405,7 +421,7 @@
"name": "python",
"nbconvert_exporter": "python",
"pygments_lexer": "ipython3",
"version": "3.8.8"
"version": "3.8.15"
}
},
"nbformat": 4,
Expand Down