From 4a37501fbd03565dca3fd01c6a9abab26a5ae1e4 Mon Sep 17 00:00:00 2001 From: alex-l-kong Date: Thu, 7 Sep 2023 11:37:24 -0700 Subject: [PATCH 1/3] Add paper citations for Albert's tiler --- templates/2_create_tiled_mibi_run.ipynb | 16 +++++++++++++++- templates/2_create_tma_mibi_run.ipynb | 20 ++++++++++++++++++-- 2 files changed, 33 insertions(+), 3 deletions(-) diff --git a/templates/2_create_tiled_mibi_run.ipynb b/templates/2_create_tiled_mibi_run.ipynb index c01ed2ac..abc2ed53 100644 --- a/templates/2_create_tiled_mibi_run.ipynb +++ b/templates/2_create_tiled_mibi_run.ipynb @@ -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": {}, @@ -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": [ + "$^1$ Tsai 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. JoVE, [OnlineFirst], https://doi.org/10.3791/65615" + ] } ], "metadata": { @@ -208,7 +222,7 @@ "name": "python", "nbconvert_exporter": "python", "pygments_lexer": "ipython3", - "version": "3.8.13" + "version": "3.8.15" } }, "nbformat": 4, diff --git a/templates/2_create_tma_mibi_run.ipynb b/templates/2_create_tma_mibi_run.ipynb index d16f7937..0301a71e 100644 --- a/templates/2_create_tma_mibi_run.ipynb +++ b/templates/2_create_tma_mibi_run.ipynb @@ -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", @@ -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": [ + "$^1$ Tsai 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. JoVE, [OnlineFirst], https://doi.org/10.3791/65615" + ] } ], "metadata": { "kernelspec": { - "display_name": "Python 3", + "display_name": "Python 3 (ipykernel)", "language": "python", "name": "python3" }, @@ -405,7 +421,7 @@ "name": "python", "nbconvert_exporter": "python", "pygments_lexer": "ipython3", - "version": "3.8.8" + "version": "3.8.15" } }, "nbformat": 4, From 5f0a64253f28fa280ee932bab28df911ef22ef26 Mon Sep 17 00:00:00 2001 From: ag-tsai <126035819+ag-tsai@users.noreply.github.com> Date: Tue, 12 Sep 2023 11:49:03 -0700 Subject: [PATCH 2/3] Update 2_create_tiled_mibi_run.ipynb Updated publication --- templates/2_create_tiled_mibi_run.ipynb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/templates/2_create_tiled_mibi_run.ipynb b/templates/2_create_tiled_mibi_run.ipynb index abc2ed53..b8cc5c65 100644 --- a/templates/2_create_tiled_mibi_run.ipynb +++ b/templates/2_create_tiled_mibi_run.ipynb @@ -202,7 +202,7 @@ "cell_type": "markdown", "metadata": {}, "source": [ - "$^1$ Tsai 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. JoVE, [OnlineFirst], https://doi.org/10.3791/65615" + "$^1$ 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. J Vis Exp, [OnlineFirst], https://www.jove.com/t/65615/rapid-setup-tissue-microarray-tiled-area-imaging-on-multiplexed-ion" ] } ], From 939f4b5d92ba180a4757f6238d398616f4973c96 Mon Sep 17 00:00:00 2001 From: ag-tsai <126035819+ag-tsai@users.noreply.github.com> Date: Tue, 12 Sep 2023 11:50:46 -0700 Subject: [PATCH 3/3] Update 2_create_tma_mibi_run.ipynb Updated publication --- templates/2_create_tma_mibi_run.ipynb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/templates/2_create_tma_mibi_run.ipynb b/templates/2_create_tma_mibi_run.ipynb index 0301a71e..31feb3b4 100644 --- a/templates/2_create_tma_mibi_run.ipynb +++ b/templates/2_create_tma_mibi_run.ipynb @@ -401,7 +401,7 @@ "id": "0cd7340c-b7d6-4f54-a8cf-2ee2e1faccb3", "metadata": {}, "source": [ - "$^1$ Tsai 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. JoVE, [OnlineFirst], https://doi.org/10.3791/65615" + "$^1$ 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. J Vis Exp, [OnlineFirst], https://www.jove.com/t/65615/rapid-setup-tissue-microarray-tiled-area-imaging-on-multiplexed-ion" ] } ],