From 90791d2ae5c0de2aa10eb1020f63026037bd7896 Mon Sep 17 00:00:00 2001 From: RussellBarkley Date: Sat, 19 Sep 2026 15:34:53 -0400 Subject: [PATCH 01/18] added a fourth viewer: find nuclei https://www.find-nuclei.com/ --- 02_approach.md | 35 ++++++++++++++++++++++++++++++----- 1 file changed, 30 insertions(+), 5 deletions(-) diff --git a/02_approach.md b/02_approach.md index 29117c75..e683e19d 100644 --- a/02_approach.md +++ b/02_approach.md @@ -16,8 +16,9 @@ Virtual microscopy. 1. Automated dataset collection with any suitable microscope Elemental Microscopy supports two interactive viewers; [Vizarr](https://github.com/hms-dbmi/vizarr) [@doi:10.1038/s41592-022-01482-7] and [OpenSeadragon](https://openseadragon.github.io/), enabling two methods of virtual microscopy based on OME-Zarr or Deep Zoom. Authors can also build custom viewers and embed them within online articles. -Brodrick developed [microATLAS](https://github.com/LadInTheLab/microATLAS-widget), which was used to view OME-Zarr data in this article. -All three viewers are readily embeddable in Elemental Microscopy. +Brodrick developed [microATLAS](https://github.com/LadInTheLab/microATLAS-widget), which was used to view OME-Zarr data in this article. +[Find Nuclei](https://www.find-nuclei.com/) is a web-based dashboard to view, analyze and share microscopy images, built on OME-Zarr. +All four viewers are embeddable in Elemental Microscopy. For Vizarr and OpenSeadragon, authors simply copy the markdown and replace the source URL with a link to their own data. For microATLAS, authors are encouraged to use the [widget builder](https://ladinthelab.github.io/microATLAS-widget/builder.html) to generate embedding code that specifies both the image and relevant customizations. @@ -33,7 +34,7 @@ As an advanced implementation of microscopy maps [@doi:10.1242/jcs.262198], pyra ```{code} markdown :label: vizarr_code :caption: Minimal markdown to embed Vizarr in Elemental Microscopy. Replace the source with your data. -:::{any:bundle} https://curvenote.github.io/widgets/widgets/vizarr-viewer.js +:::{anywidget} https://curvenote.github.io/widgets/widgets/vizarr-viewer.js { "source": "https://your-bucket.s3.amazonaws.com/sample.zarr/", "height": "600px" @@ -46,7 +47,7 @@ As an advanced implementation of microscopy maps [@doi:10.1242/jcs.262198], pyra ```{code} markdown :label: microatlas_code :caption: Example markdown to embed microATLAS in Elemental Microscopy. Create your own with the [builder](https://ladinthelab.github.io/microATLAS-widget/builder.html). -:::{any:bundle} https://ladinthelab.github.io/microATLAS-widget/widget.js +:::{anywidget} microatlas-local.mjs { "source": "https://your-bucket.s3.amazonaws.com/sample.zarr/", "views": [ @@ -71,6 +72,30 @@ Use the menu (☰, top-left corner) to change the displayed channels, colours, o Scroll (↕) to zoom into cells of interest. ``` +### Find Nuclei + +:::{any:bundle} https://find-nuclei.github.io/embed/v1/widget.mjs +{ + "url": "https://nyu1.osn.mghpcc.org/barkley-replication/nuclei_mosaic.zarr", + "channels": "0:on:FFFFFF:0:240", + "x": 2115, "y": 1688, "zoom": -1.9, + "height": "500" +} +::: + +```{code} markdown +:label: findnuclei_code +:caption: Example markdown to embed Find Nuclei in Elemental Microscopy. +:::{any:bundle} https://find-nuclei.github.io/embed/v1/widget.mjs +{ + "url": "https://nyu1.osn.mghpcc.org/barkley-replication/nuclei_mosaic.zarr", + "channels": "0:on:FFFFFF:0:240", + "x": 2115, "y": 1688, "zoom": -1.9, + "height": "500" +} +::: +``` + ## Deep Zoom [Deep Zoom]() is a free and open-source solution, described elsewhere [@doi:10.1242/jcs.262198], now embeddable in Elemental Microscopy. @@ -82,7 +107,7 @@ By default, readers cannot control dimensions like channels or time, so it is be ```{code} markdown :label: openseadragon_code :caption: Minimal markdown to embed OpenSeadragon in Elemental Microscopy. Replace the source with your DZI. -:::{any:bundle} https://curvenote.github.io/widgets/widgets/openseadragon.mjs +:::{anywidget} https://curvenote.github.io/widgets/widgets/openseadragon.mjs { "tileSources": "https://your-github.github.io/your-repository/sample.dzi" } From 29998ed00617140c9e8a8c7f3637680df492b8a2 Mon Sep 17 00:00:00 2001 From: RussellBarkley Date: Sat, 19 Sep 2026 16:23:09 -0400 Subject: [PATCH 02/18] embedding nuclei with 3 viewers --- 02_approach.md | 68 +++++++++++++++++++++++++++++++++++++++----------- 1 file changed, 54 insertions(+), 14 deletions(-) diff --git a/02_approach.md b/02_approach.md index e683e19d..3f135526 100644 --- a/02_approach.md +++ b/02_approach.md @@ -17,7 +17,7 @@ Virtual microscopy. 1. Automated dataset collection with any suitable microscope Elemental Microscopy supports two interactive viewers; [Vizarr](https://github.com/hms-dbmi/vizarr) [@doi:10.1038/s41592-022-01482-7] and [OpenSeadragon](https://openseadragon.github.io/), enabling two methods of virtual microscopy based on OME-Zarr or Deep Zoom. Authors can also build custom viewers and embed them within online articles. Brodrick developed [microATLAS](https://github.com/LadInTheLab/microATLAS-widget), which was used to view OME-Zarr data in this article. -[Find Nuclei](https://www.find-nuclei.com/) is a web-based dashboard to view, analyze and share microscopy images, built on OME-Zarr. +[Find Nuclei](https://www.find-nuclei.com/) is a web-based dashboard to organize, analyze and share bioimages, built on OME-Zarr. All four viewers are embeddable in Elemental Microscopy. For Vizarr and OpenSeadragon, authors simply copy the markdown and replace the source URL with a link to their own data. For microATLAS, authors are encouraged to use the [widget builder](https://ladinthelab.github.io/microATLAS-widget/builder.html) to generate embedding code that specifies both the image and relevant customizations. @@ -29,27 +29,73 @@ Most native microscopy file formats can be converted to OME-Zarr with preserved It is a chunked file type that can support multiple resolution levels. As an advanced implementation of microscopy maps [@doi:10.1242/jcs.262198], pyramidal OME-Zarr data can be viewed online [@doi:10.1038/s41592-022-01482-7]. -### Vizarr +### Vizarr viewer + +:::{anywidget} https://curvenote.github.io/widgets/widgets/vizarr-viewer.js +{ + "source": "https://nyu1.osn.mghpcc.org/barkley-replication/nuclei_mosaic.zarr", + "height": "600px" +} +::: ```{code} markdown :label: vizarr_code :caption: Minimal markdown to embed Vizarr in Elemental Microscopy. Replace the source with your data. :::{anywidget} https://curvenote.github.io/widgets/widgets/vizarr-viewer.js { - "source": "https://your-bucket.s3.amazonaws.com/sample.zarr/", + "source": "https://nyu1.osn.mghpcc.org/barkley-replication/nuclei_mosaic.zarr", "height": "600px" } ::: ``` -### microATLAS +### microATLAS viewer + +:::{anywidget} microatlas-local.mjs +{ + "source": "https://nyu1.osn.mghpcc.org/barkley-replication/nuclei_mosaic.zarr", + "width": "600px", + "height": "600px", + "views": [ + { + "name": "inferno", + "zoom": -2.866, + "target": [ + 137103, + 166506, + 0 + ], + "appearance": { + "channelsVisible": [ + true + ], + "channelColors": [ + [ + 255, + 255, + 255 + ] + ], + "contrastLimits": [ + [ + 0, + 255 + ] + ], + "blendMode": "merged", + "colormap": "inferno" + } + } + ] +} +::: ```{code} markdown :label: microatlas_code :caption: Example markdown to embed microATLAS in Elemental Microscopy. Create your own with the [builder](https://ladinthelab.github.io/microATLAS-widget/builder.html). :::{anywidget} microatlas-local.mjs { - "source": "https://your-bucket.s3.amazonaws.com/sample.zarr/", + "source": "https://nyu1.osn.mghpcc.org/barkley-replication/nuclei_mosaic.zarr", "views": [ { "name": "Overview", @@ -65,21 +111,15 @@ As an advanced implementation of microscopy maps [@doi:10.1242/jcs.262198], pyra ::: ``` -```{figure} ./thumbnail.gif -:label: demo -Interacting with microATLAS: -Use the menu (☰, top-left corner) to change the displayed channels, colours, or contrast. -Scroll (↕) to zoom into cells of interest. -``` - -### Find Nuclei +### Find Nuclei viewer :::{any:bundle} https://find-nuclei.github.io/embed/v1/widget.mjs { "url": "https://nyu1.osn.mghpcc.org/barkley-replication/nuclei_mosaic.zarr", "channels": "0:on:FFFFFF:0:240", "x": 2115, "y": 1688, "zoom": -1.9, - "height": "500" + "height": "600" + "invert": true } ::: From ba23e0f6b3ebd0040e1eeaedb239500b6d2bb28c Mon Sep 17 00:00:00 2001 From: RussellBarkley Date: Sat, 19 Sep 2026 16:26:56 -0400 Subject: [PATCH 03/18] add comma --- 02_approach.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/02_approach.md b/02_approach.md index 3f135526..00ce8445 100644 --- a/02_approach.md +++ b/02_approach.md @@ -118,7 +118,7 @@ As an advanced implementation of microscopy maps [@doi:10.1242/jcs.262198], pyra "url": "https://nyu1.osn.mghpcc.org/barkley-replication/nuclei_mosaic.zarr", "channels": "0:on:FFFFFF:0:240", "x": 2115, "y": 1688, "zoom": -1.9, - "height": "600" + "height": "600", "invert": true } ::: From 140b1d2610de89ea2c70adb221c9f16123eb6f18 Mon Sep 17 00:00:00 2001 From: RussellBarkley Date: Sat, 19 Sep 2026 16:30:06 -0400 Subject: [PATCH 04/18] anywidget to any:bundle --- 02_approach.md | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/02_approach.md b/02_approach.md index 00ce8445..05b6a90b 100644 --- a/02_approach.md +++ b/02_approach.md @@ -31,7 +31,7 @@ As an advanced implementation of microscopy maps [@doi:10.1242/jcs.262198], pyra ### Vizarr viewer -:::{anywidget} https://curvenote.github.io/widgets/widgets/vizarr-viewer.js +:::{any:bundle} https://curvenote.github.io/widgets/widgets/vizarr-viewer.js { "source": "https://nyu1.osn.mghpcc.org/barkley-replication/nuclei_mosaic.zarr", "height": "600px" @@ -51,7 +51,7 @@ As an advanced implementation of microscopy maps [@doi:10.1242/jcs.262198], pyra ### microATLAS viewer -:::{anywidget} microatlas-local.mjs +:::{any:bundle} microatlas-local.mjs { "source": "https://nyu1.osn.mghpcc.org/barkley-replication/nuclei_mosaic.zarr", "width": "600px", From d3711e6bf8ab6c6fbb4df742c0ec542dee551570 Mon Sep 17 00:00:00 2001 From: RussellBarkley Date: Sat, 19 Sep 2026 16:37:32 -0400 Subject: [PATCH 05/18] Update 02_approach.md --- 02_approach.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/02_approach.md b/02_approach.md index 05b6a90b..9ffadf43 100644 --- a/02_approach.md +++ b/02_approach.md @@ -51,7 +51,7 @@ As an advanced implementation of microscopy maps [@doi:10.1242/jcs.262198], pyra ### microATLAS viewer -:::{any:bundle} microatlas-local.mjs +:::{any:bundle} https://LadInTheLab.github.io/microATLAS-widget/widget.js { "source": "https://nyu1.osn.mghpcc.org/barkley-replication/nuclei_mosaic.zarr", "width": "600px", From a2ecb40f91e483cca70a25fa014f364c5dea7da9 Mon Sep 17 00:00:00 2001 From: RussellBarkley Date: Sat, 19 Sep 2026 16:45:55 -0400 Subject: [PATCH 06/18] default inferno for microatlas, iframe for vizarr vizarr did not load because multiple deck.gl copies on the same page with different versions --- 02_approach.md | 12 +++++------- 1 file changed, 5 insertions(+), 7 deletions(-) diff --git a/02_approach.md b/02_approach.md index 9ffadf43..ae20dc42 100644 --- a/02_approach.md +++ b/02_approach.md @@ -31,12 +31,9 @@ As an advanced implementation of microscopy maps [@doi:10.1242/jcs.262198], pyra ### Vizarr viewer -:::{any:bundle} https://curvenote.github.io/widgets/widgets/vizarr-viewer.js -{ - "source": "https://nyu1.osn.mghpcc.org/barkley-replication/nuclei_mosaic.zarr", - "height": "600px" -} -::: +```{iframe} https://hms-dbmi.github.io/vizarr/?source=https://nyu1.osn.mghpcc.org/barkley-replication/nuclei_mosaic.zarr&viewState={%22target%22:[124547.79378129813,32310.74580437236],%22zoom%22:-3.8361114954494266} +:width: 100% +``` ```{code} markdown :label: vizarr_code @@ -84,7 +81,8 @@ As an advanced implementation of microscopy maps [@doi:10.1242/jcs.262198], pyra ], "blendMode": "merged", "colormap": "inferno" - } + }, + "default": true } ] } From 09961674bd29cf86f8acfc0951b0129c7e46272f Mon Sep 17 00:00:00 2001 From: RussellBarkley Date: Sat, 19 Sep 2026 17:03:09 -0400 Subject: [PATCH 07/18] add openseadragon --- 02_approach.md | 64 +++++++++++++++++++++++++++++++++++++------------- 1 file changed, 48 insertions(+), 16 deletions(-) diff --git a/02_approach.md b/02_approach.md index ae20dc42..84b66b80 100644 --- a/02_approach.md +++ b/02_approach.md @@ -29,7 +29,7 @@ Most native microscopy file formats can be converted to OME-Zarr with preserved It is a chunked file type that can support multiple resolution levels. As an advanced implementation of microscopy maps [@doi:10.1242/jcs.262198], pyramidal OME-Zarr data can be viewed online [@doi:10.1038/s41592-022-01482-7]. -### Vizarr viewer +### Vizarr ```{iframe} https://hms-dbmi.github.io/vizarr/?source=https://nyu1.osn.mghpcc.org/barkley-replication/nuclei_mosaic.zarr&viewState={%22target%22:[124547.79378129813,32310.74580437236],%22zoom%22:-3.8361114954494266} :width: 100% @@ -38,7 +38,7 @@ As an advanced implementation of microscopy maps [@doi:10.1242/jcs.262198], pyra ```{code} markdown :label: vizarr_code :caption: Minimal markdown to embed Vizarr in Elemental Microscopy. Replace the source with your data. -:::{anywidget} https://curvenote.github.io/widgets/widgets/vizarr-viewer.js +:::{any:bundle} https://curvenote.github.io/widgets/widgets/vizarr-viewer.js { "source": "https://nyu1.osn.mghpcc.org/barkley-replication/nuclei_mosaic.zarr", "height": "600px" @@ -46,7 +46,7 @@ As an advanced implementation of microscopy maps [@doi:10.1242/jcs.262198], pyra ::: ``` -### microATLAS viewer +### microATLAS :::{any:bundle} https://LadInTheLab.github.io/microATLAS-widget/widget.js { @@ -91,25 +91,48 @@ As an advanced implementation of microscopy maps [@doi:10.1242/jcs.262198], pyra ```{code} markdown :label: microatlas_code :caption: Example markdown to embed microATLAS in Elemental Microscopy. Create your own with the [builder](https://ladinthelab.github.io/microATLAS-widget/builder.html). -:::{anywidget} microatlas-local.mjs +:::{any:bundle} https://LadInTheLab.github.io/microATLAS-widget/widget.js { "source": "https://nyu1.osn.mghpcc.org/barkley-replication/nuclei_mosaic.zarr", + "width": "600px", + "height": "600px", "views": [ { - "name": "Overview", - "zoom": -4, - "target": [4886, 4886, 0] + "name": "inferno", + "zoom": -2.866, + "target": [ + 137103, + 166506, + 0 + ], + "appearance": { + "channelsVisible": [ + true + ], + "channelColors": [ + [ + 255, + 255, + 255 + ] + ], + "contrastLimits": [ + [ + 0, + 255 + ] + ], + "blendMode": "merged", + "colormap": "inferno" + }, + "default": true } - ], - "annotations": [ - { "name": "Region A", "target": [2400, 2400], "color": [100, 200, 255] } - ], - "scaleBar": { "maxWidth": 120, "position": "bottom-right" } + ] } ::: ``` -### Find Nuclei viewer +### Find Nuclei :::{any:bundle} https://find-nuclei.github.io/embed/v1/widget.mjs { @@ -129,7 +152,8 @@ As an advanced implementation of microscopy maps [@doi:10.1242/jcs.262198], pyra "url": "https://nyu1.osn.mghpcc.org/barkley-replication/nuclei_mosaic.zarr", "channels": "0:on:FFFFFF:0:240", "x": 2115, "y": 1688, "zoom": -1.9, - "height": "500" + "height": "600", + "invert": true } ::: ``` @@ -142,12 +166,20 @@ By default, readers cannot control dimensions like channels or time, so it is be ### OpenSeadragon +:label: openseadragon_code +:caption: Minimal markdown to embed OpenSeadragon in Elemental Microscopy. Replace the source with your DZI. +:::{any:bundle} https://curvenote.github.io/widgets/widgets/openseadragon.mjs +{ + "tileSources": "https://russellbarkley.github.io/nucleusnet-10k/nucleusnet_10k.dzi" +} +::: + ```{code} markdown :label: openseadragon_code :caption: Minimal markdown to embed OpenSeadragon in Elemental Microscopy. Replace the source with your DZI. -:::{anywidget} https://curvenote.github.io/widgets/widgets/openseadragon.mjs +:::{any:bundle} https://curvenote.github.io/widgets/widgets/openseadragon.mjs { - "tileSources": "https://your-github.github.io/your-repository/sample.dzi" + "tileSources": "https://russellbarkley.github.io/nucleusnet-10k/nucleusnet_10k.dzi" } ::: ``` From 3ed5e8209865e42cf4341b7af05952941f4d114e Mon Sep 17 00:00:00 2001 From: RussellBarkley Date: Sat, 19 Sep 2026 17:30:17 -0400 Subject: [PATCH 08/18] Update 02_approach.md --- 02_approach.md | 40 +++------------------------------------- 1 file changed, 3 insertions(+), 37 deletions(-) diff --git a/02_approach.md b/02_approach.md index 84b66b80..8e5273d1 100644 --- a/02_approach.md +++ b/02_approach.md @@ -17,8 +17,8 @@ Virtual microscopy. 1. Automated dataset collection with any suitable microscope Elemental Microscopy supports two interactive viewers; [Vizarr](https://github.com/hms-dbmi/vizarr) [@doi:10.1038/s41592-022-01482-7] and [OpenSeadragon](https://openseadragon.github.io/), enabling two methods of virtual microscopy based on OME-Zarr or Deep Zoom. Authors can also build custom viewers and embed them within online articles. Brodrick developed [microATLAS](https://github.com/LadInTheLab/microATLAS-widget), which was used to view OME-Zarr data in this article. -[Find Nuclei](https://www.find-nuclei.com/) is a web-based dashboard to organize, analyze and share bioimages, built on OME-Zarr. -All four viewers are embeddable in Elemental Microscopy. +[Find Nuclei](https://www.find-nuclei.com/) is a web-based dashboard to view, analyze, and share OME-Zarr bioimages. +All four viewers are embeddable in Elemental Microscopy articles. For Vizarr and OpenSeadragon, authors simply copy the markdown and replace the source URL with a link to their own data. For microATLAS, authors are encouraged to use the [widget builder](https://ladinthelab.github.io/microATLAS-widget/builder.html) to generate embedding code that specifies both the image and relevant customizations. @@ -95,39 +95,7 @@ As an advanced implementation of microscopy maps [@doi:10.1242/jcs.262198], pyra { "source": "https://nyu1.osn.mghpcc.org/barkley-replication/nuclei_mosaic.zarr", "width": "600px", - "height": "600px", - "views": [ - { - "name": "inferno", - "zoom": -2.866, - "target": [ - 137103, - 166506, - 0 - ], - "appearance": { - "channelsVisible": [ - true - ], - "channelColors": [ - [ - 255, - 255, - 255 - ] - ], - "contrastLimits": [ - [ - 0, - 255 - ] - ], - "blendMode": "merged", - "colormap": "inferno" - }, - "default": true - } - ] + "height": "600px" } ::: ``` @@ -166,8 +134,6 @@ By default, readers cannot control dimensions like channels or time, so it is be ### OpenSeadragon -:label: openseadragon_code -:caption: Minimal markdown to embed OpenSeadragon in Elemental Microscopy. Replace the source with your DZI. :::{any:bundle} https://curvenote.github.io/widgets/widgets/openseadragon.mjs { "tileSources": "https://russellbarkley.github.io/nucleusnet-10k/nucleusnet_10k.dzi" From a5fea9dfaa7e8ae26adfb9917f054b267b4ad440 Mon Sep 17 00:00:00 2001 From: RussellBarkley Date: Sat, 19 Sep 2026 17:57:54 -0400 Subject: [PATCH 09/18] referencing findnuclei --- 02_approach.md | 10 ++-------- 03_model.md | 6 ++++++ references.bib | 9 +++++++++ 3 files changed, 17 insertions(+), 8 deletions(-) create mode 100644 references.bib diff --git a/02_approach.md b/02_approach.md index 8e5273d1..95e8db84 100644 --- a/02_approach.md +++ b/02_approach.md @@ -17,7 +17,7 @@ Virtual microscopy. 1. Automated dataset collection with any suitable microscope Elemental Microscopy supports two interactive viewers; [Vizarr](https://github.com/hms-dbmi/vizarr) [@doi:10.1038/s41592-022-01482-7] and [OpenSeadragon](https://openseadragon.github.io/), enabling two methods of virtual microscopy based on OME-Zarr or Deep Zoom. Authors can also build custom viewers and embed them within online articles. Brodrick developed [microATLAS](https://github.com/LadInTheLab/microATLAS-widget), which was used to view OME-Zarr data in this article. -[Find Nuclei](https://www.find-nuclei.com/) is a web-based dashboard to view, analyze, and share OME-Zarr bioimages. +[Find Nuclei](https://www.find-nuclei.com/) provides a web-based dashboard of tools and infrastructure for working with OME-Zarr bioimages [@FindNuclei2026]. All four viewers are embeddable in Elemental Microscopy articles. For Vizarr and OpenSeadragon, authors simply copy the markdown and replace the source URL with a link to their own data. For microATLAS, authors are encouraged to use the [widget builder](https://ladinthelab.github.io/microATLAS-widget/builder.html) to generate embedding code that specifies both the image and relevant customizations. @@ -114,7 +114,7 @@ As an advanced implementation of microscopy maps [@doi:10.1242/jcs.262198], pyra ```{code} markdown :label: findnuclei_code -:caption: Example markdown to embed Find Nuclei in Elemental Microscopy. +:caption: Example markdown to embed [Find Nuclei](https://www.find-nuclei.com/) in Elemental Microscopy [@FindNuclei2026]. :::{any:bundle} https://find-nuclei.github.io/embed/v1/widget.mjs { "url": "https://nyu1.osn.mghpcc.org/barkley-replication/nuclei_mosaic.zarr", @@ -149,9 +149,3 @@ By default, readers cannot control dimensions like channels or time, so it is be } ::: ``` - -## Imaging -Data collection was fully motorized for unbiased sampling of large panoramas from replicate immunofluorescence experiments. -Grids of overlapping tiles were acquired with a robotic XY stage (IX3-SSU) and Z-drift compensation (IX3-ZDC). -Coverslips were imaged with an Olympus Fluoview FV3000 confocal microscope using a 100X objective lens (Olympus model UPLAPO100X, NA 1.50) in immersion oil. -Pinholes in each channel were maximized to capture the widest depth of field. \ No newline at end of file diff --git a/03_model.md b/03_model.md index de970a0f..b2e72abc 100644 --- a/03_model.md +++ b/03_model.md @@ -22,3 +22,9 @@ In the results, Barkley annotated transfected cells by infection status to compa ### Cells HeLa CCL-2 cells were cultured in Dulbecco’s modification of Eagle’s Medium (DMEM) (50-003-PB, Corning) supplemented with 10% fetal bovine serum (FS-0500-AD, Atlas). Antibiotics were not used in the replication study, although the original study used 100 U/ml penicillin G, 100μg/ml streptomycin and 0.25μg/ml amphotericin B. + +### Imaging +Data collection was fully motorized for unbiased sampling of large panoramas from replicate immunofluorescence experiments. +Grids of overlapping tiles were acquired with a robotic XY stage (IX3-SSU) and Z-drift compensation (IX3-ZDC). +Coverslips were imaged with an Olympus Fluoview FV3000 confocal microscope using a 100X objective lens (Olympus model UPLAPO100X, NA 1.50) in immersion oil. +Pinholes in each channel were maximized to capture the widest depth of field. diff --git a/references.bib b/references.bib new file mode 100644 index 00000000..e1567f1f --- /dev/null +++ b/references.bib @@ -0,0 +1,9 @@ +@misc{FindNuclei2026, + author = {{Find Nuclei}}, + title = {Find Nuclei Viewer}, + year = {2026}, + month = {9}, + version = {2026-09-19}, + url = {https://find-nuclei.github.io}, + note = {Software, version 2026-09-19. Source code: https://github.com/Find-Nuclei/find-nuclei.github.io}, +} From 0443b88c1ee8421459ea43da859dd9ed4040e302 Mon Sep 17 00:00:00 2001 From: RussellBarkley Date: Sat, 19 Sep 2026 18:30:38 -0400 Subject: [PATCH 10/18] Update 02_approach.md --- 02_approach.md | 6 ++++-- 1 file changed, 4 insertions(+), 2 deletions(-) diff --git a/02_approach.md b/02_approach.md index 95e8db84..594539ae 100644 --- a/02_approach.md +++ b/02_approach.md @@ -7,7 +7,9 @@ numbering: Already adopted by some clinicians and educators, virtual microscopy could also benefit researchers as an interface for communicating and interpreting image data. Indeed, interactive microscopy maps were first proposed for this purpose — as an unbiased way to present electron microscopy data [@doi:10.1083/jcb.201201140]. Free and open-source solutions [@doi:10.1242/jcs.262198] and recent advances in file formats [@doi:10.1007/s00418-023-02209-1] now make this feasible, yet these tools have not been used in scientific publishing. -Our approach combined automated image acquisition, multi-scale [pyramid]() formats and embedded interactive viewers ([](#abstract)). +Most journals publish articles as static pages that cannot run code, so interactive figures must be provided as links to external pages. +To our knowledge, Elemental Microscopy is the first journal that allows interactive viewers to be embedded directly within the article. +Our approach to virtual microscopy combined automated image acquisition, multi-scale [pyramid]() formats and embedded interactive viewers ([](#abstract)). ```{figure} ./figures/Virtual_microscopy.png :label: abstract @@ -18,7 +20,7 @@ Elemental Microscopy supports two interactive viewers; [Vizarr](https://github.c Authors can also build custom viewers and embed them within online articles. Brodrick developed [microATLAS](https://github.com/LadInTheLab/microATLAS-widget), which was used to view OME-Zarr data in this article. [Find Nuclei](https://www.find-nuclei.com/) provides a web-based dashboard of tools and infrastructure for working with OME-Zarr bioimages [@FindNuclei2026]. -All four viewers are embeddable in Elemental Microscopy articles. +All four viewers are embeddable in Elemental Microscopy. For Vizarr and OpenSeadragon, authors simply copy the markdown and replace the source URL with a link to their own data. For microATLAS, authors are encouraged to use the [widget builder](https://ladinthelab.github.io/microATLAS-widget/builder.html) to generate embedding code that specifies both the image and relevant customizations. From cea61fa81bb53139236f32e3e28ebbe129b869ed Mon Sep 17 00:00:00 2001 From: RussellBarkley Date: Sat, 19 Sep 2026 18:37:09 -0400 Subject: [PATCH 11/18] Update 02_approach.md --- 02_approach.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/02_approach.md b/02_approach.md index 594539ae..dc773119 100644 --- a/02_approach.md +++ b/02_approach.md @@ -8,7 +8,7 @@ Already adopted by some clinicians and educators, virtual microscopy could also Indeed, interactive microscopy maps were first proposed for this purpose — as an unbiased way to present electron microscopy data [@doi:10.1083/jcb.201201140]. Free and open-source solutions [@doi:10.1242/jcs.262198] and recent advances in file formats [@doi:10.1007/s00418-023-02209-1] now make this feasible, yet these tools have not been used in scientific publishing. Most journals publish articles as static pages that cannot run code, so interactive figures must be provided as links to external pages. -To our knowledge, Elemental Microscopy is the first journal that allows interactive viewers to be embedded directly within the article. +To our knowledge, Elemental Microscopy is among the first journals that allows interactive viewers to be embedded directly within the article. Our approach to virtual microscopy combined automated image acquisition, multi-scale [pyramid]() formats and embedded interactive viewers ([](#abstract)). ```{figure} ./figures/Virtual_microscopy.png From 9f29b0810c8660e0044cd2b85b11d6f4c204ab65 Mon Sep 17 00:00:00 2001 From: RussellBarkley Date: Thu, 29 Oct 2026 15:45:07 -0400 Subject: [PATCH 12/18] Update 02_approach.md --- 02_approach.md | 26 +++++++++++++++----------- 1 file changed, 15 insertions(+), 11 deletions(-) diff --git a/02_approach.md b/02_approach.md index dc773119..d33f6750 100644 --- a/02_approach.md +++ b/02_approach.md @@ -5,24 +5,28 @@ numbering: --- Already adopted by some clinicians and educators, virtual microscopy could also benefit researchers as an interface for communicating and interpreting image data. -Indeed, interactive microscopy maps were first proposed for this purpose — as an unbiased way to present electron microscopy data [@doi:10.1083/jcb.201201140]. -Free and open-source solutions [@doi:10.1242/jcs.262198] and recent advances in file formats [@doi:10.1007/s00418-023-02209-1] now make this feasible, yet these tools have not been used in scientific publishing. +Indeed, interactive microscopy maps were proposed as an unbiased way to present electron microscopy data [@doi:10.1083/jcb.201201140]. +Free and open-source solutions [@doi:10.1242/jcs.262198] and recent advances in file formats [@doi:10.1007/s00418-023-02209-1] now make this feasible, yet virtual microscopy remains rare in scientific publishing. Most journals publish articles as static pages that cannot run code, so interactive figures must be provided as links to external pages. -To our knowledge, Elemental Microscopy is among the first journals that allows interactive viewers to be embedded directly within the article. -Our approach to virtual microscopy combined automated image acquisition, multi-scale [pyramid]() formats and embedded interactive viewers ([](#abstract)). +Even Elsevier's Virtual Microscope, developed for high-resolution pathology images, is opened from links in figure captions. +To our knowledge, Elemental Microscopy is among the first journals that allows interactive viewers to be embedded directly within the article, so that each figure is a live view of the full-resolution dataset rather than a static rendering of it. +Here we describe a workflow for this kind of virtual microscopy: datasets are acquired automatically, converted to multi-scale [pyramid]() formats, hosted in the cloud, and streamed to viewers embedded in the article ([](#abstract)). ```{figure} ./figures/Virtual_microscopy.png :label: abstract Virtual microscopy. 1. Automated dataset collection with any suitable microscope. ZDC: Z-drift compensation. 2. Stitch tiles then convert the image to DZI or OME-Zarr, host online. 3. Image tiles or data chunks are retrieved from cloud storage as readers interact with microscopy maps. ``` -Elemental Microscopy supports two interactive viewers; [Vizarr](https://github.com/hms-dbmi/vizarr) [@doi:10.1038/s41592-022-01482-7] and [OpenSeadragon](https://openseadragon.github.io/), enabling two methods of virtual microscopy based on OME-Zarr or Deep Zoom. -Authors can also build custom viewers and embed them within online articles. -Brodrick developed [microATLAS](https://github.com/LadInTheLab/microATLAS-widget), which was used to view OME-Zarr data in this article. -[Find Nuclei](https://www.find-nuclei.com/) provides a web-based dashboard of tools and infrastructure for working with OME-Zarr bioimages [@FindNuclei2026]. -All four viewers are embeddable in Elemental Microscopy. -For Vizarr and OpenSeadragon, authors simply copy the markdown and replace the source URL with a link to their own data. -For microATLAS, authors are encouraged to use the [widget builder](https://ladinthelab.github.io/microATLAS-widget/builder.html) to generate embedding code that specifies both the image and relevant customizations. +Elemental Microscopy natively supports two interactive viewers; [Vizarr](https://github.com/hms-dbmi/vizarr) [@doi:10.1038/s41592-022-01482-7] and [OpenSeadragon](https://openseadragon.github.io/), which enable virtual microscopy of OME-Zarr and Deep Zoom images, respectively. +To use either viewer, authors copy the provided markdown and replace the source URL with a link to their own data. +Authors can also build custom viewers and embed them within their online articles. +Brodrick developed [microATLAS](https://github.com/LadInTheLab/microATLAS-widget) to present the large multiplexed immunofluorescence datasets in this article, and its [widget builder](https://ladinthelab.github.io/microATLAS-widget/builder.html) generates embedding code that specifies both the image and its display settings. +A third route is to integrate existing open-source viewers. +In collaboration with the developers of [Find Nuclei](https://www.find-nuclei.com/), a browser-based dashboard for OME-Zarr datasets [@FindNuclei2026], we made their viewer embeddable in Elemental Microscopy. +Its toolbar embed button (<>) generates MyST code to embed the current view. + +To compare these viewers, we embed each one below with the same dataset: a mosaic of roughly one million nucleus images [@doi:10.5281/zenodo.18776682] in OME-Zarr, and a 10,000-image subset in Deep Zoom. +This nucleus dataset was not analyzed in this article; it was included only to demonstrate how each viewer handles a very large image. ## OME-Zarr From 7fad9192b650565d0ed067798040f8b5f5f4b9ec Mon Sep 17 00:00:00 2001 From: RussellBarkley Date: Thu, 29 Oct 2026 18:54:20 -0400 Subject: [PATCH 13/18] Update 02_approach.md --- 02_approach.md | 13 +++++++------ 1 file changed, 7 insertions(+), 6 deletions(-) diff --git a/02_approach.md b/02_approach.md index d33f6750..f3fe73bc 100644 --- a/02_approach.md +++ b/02_approach.md @@ -8,7 +8,7 @@ Already adopted by some clinicians and educators, virtual microscopy could also Indeed, interactive microscopy maps were proposed as an unbiased way to present electron microscopy data [@doi:10.1083/jcb.201201140]. Free and open-source solutions [@doi:10.1242/jcs.262198] and recent advances in file formats [@doi:10.1007/s00418-023-02209-1] now make this feasible, yet virtual microscopy remains rare in scientific publishing. Most journals publish articles as static pages that cannot run code, so interactive figures must be provided as links to external pages. -Even Elsevier's Virtual Microscope, developed for high-resolution pathology images, is opened from links in figure captions. +Even [Elsevier's Virtual Microscope](https://www-prod.elsevier.com/researcher/author/tools-and-resources/data-visualization/virtual-microscope) is opened from links in figure captions. To our knowledge, Elemental Microscopy is among the first journals that allows interactive viewers to be embedded directly within the article, so that each figure is a live view of the full-resolution dataset rather than a static rendering of it. Here we describe a workflow for this kind of virtual microscopy: datasets are acquired automatically, converted to multi-scale [pyramid]() formats, hosted in the cloud, and streamed to viewers embedded in the article ([](#abstract)). @@ -21,12 +21,13 @@ Elemental Microscopy natively supports two interactive viewers; [Vizarr](https:/ To use either viewer, authors copy the provided markdown and replace the source URL with a link to their own data. Authors can also build custom viewers and embed them within their online articles. Brodrick developed [microATLAS](https://github.com/LadInTheLab/microATLAS-widget) to present the large multiplexed immunofluorescence datasets in this article, and its [widget builder](https://ladinthelab.github.io/microATLAS-widget/builder.html) generates embedding code that specifies both the image and its display settings. -A third route is to integrate existing open-source viewers. -In collaboration with the developers of [Find Nuclei](https://www.find-nuclei.com/), a browser-based dashboard for OME-Zarr datasets [@FindNuclei2026], we made their viewer embeddable in Elemental Microscopy. -Its toolbar embed button (<>) generates MyST code to embed the current view. +We also collaborated with the developers of [Find Nuclei](https://www.find-nuclei.com/), a browser-based dashboard for OME-Zarr datasets, so that its toolbar embed button generates MyST code for embedding the viewer in Elemental Microscopy articles [@FindNuclei2026]. -To compare these viewers, we embed each one below with the same dataset: a mosaic of roughly one million nucleus images [@doi:10.5281/zenodo.18776682] in OME-Zarr, and a 10,000-image subset in Deep Zoom. -This nucleus dataset was not analyzed in this article; it was included only to demonstrate how each viewer handles a very large image. +The four figures below are interactive microscopy maps for readers to try, each showing the same demonstration sataset: a mosaic of roughly one million nucleus images [@doi:10.5281/zenodo.18776682]. +This data is not analyzed in this article; it is included only to show how each viewer handles very large data. +Three figures stream OME-Zarr data from cloud object storage to Vizarr, microATLAS and Find Nuclei, while the fourth streams a smaller Deep Zoom (DZI) subset from GitHub Pages to OpenSeadragon. +Each viewer is embedded with a single MyST directive, shown below its figure. +For Vizarr and OpenSeadragon, authors replace the source URL with a link to their own data, while microATLAS and Find Nuclei generate the embedding code for a chosen view, so adding an interactive figure amounts to pasting a short block of markup. ## OME-Zarr From 3da44da0bb30753a8245b1bdf2bd11cb07ce66a3 Mon Sep 17 00:00:00 2001 From: RussellBarkley Date: Thu, 29 Oct 2026 19:02:43 -0400 Subject: [PATCH 14/18] Update 02_approach.md --- 02_approach.md | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/02_approach.md b/02_approach.md index f3fe73bc..9b48e697 100644 --- a/02_approach.md +++ b/02_approach.md @@ -9,8 +9,8 @@ Indeed, interactive microscopy maps were proposed as an unbiased way to present Free and open-source solutions [@doi:10.1242/jcs.262198] and recent advances in file formats [@doi:10.1007/s00418-023-02209-1] now make this feasible, yet virtual microscopy remains rare in scientific publishing. Most journals publish articles as static pages that cannot run code, so interactive figures must be provided as links to external pages. Even [Elsevier's Virtual Microscope](https://www-prod.elsevier.com/researcher/author/tools-and-resources/data-visualization/virtual-microscope) is opened from links in figure captions. -To our knowledge, Elemental Microscopy is among the first journals that allows interactive viewers to be embedded directly within the article, so that each figure is a live view of the full-resolution dataset rather than a static rendering of it. -Here we describe a workflow for this kind of virtual microscopy: datasets are acquired automatically, converted to multi-scale [pyramid]() formats, hosted in the cloud, and streamed to viewers embedded in the article ([](#abstract)). +To our knowledge, Elemental Microscopy is among the first journals that allows interactive viewers to be embedded directly within the article, so each figure is a live view of the full-resolution dataset rather than a static rendering. +Here we describe a workflow for this kind of virtual microscopy: datasets are acquired automatically, converted to multi-scale [pyramid]() formats, hosted in the cloud, and streamed to viewers embedded in a paper ([](#abstract)). ```{figure} ./figures/Virtual_microscopy.png :label: abstract @@ -23,11 +23,11 @@ Authors can also build custom viewers and embed them within their online article Brodrick developed [microATLAS](https://github.com/LadInTheLab/microATLAS-widget) to present the large multiplexed immunofluorescence datasets in this article, and its [widget builder](https://ladinthelab.github.io/microATLAS-widget/builder.html) generates embedding code that specifies both the image and its display settings. We also collaborated with the developers of [Find Nuclei](https://www.find-nuclei.com/), a browser-based dashboard for OME-Zarr datasets, so that its toolbar embed button generates MyST code for embedding the viewer in Elemental Microscopy articles [@FindNuclei2026]. -The four figures below are interactive microscopy maps for readers to try, each showing the same demonstration sataset: a mosaic of roughly one million nucleus images [@doi:10.5281/zenodo.18776682]. +The four figures below are interactive microscopy maps for readers to try, each showing the same demonstration dataset: a mosaic of roughly one million nucleus images [@doi:10.5281/zenodo.18776682]. This data is not analyzed in this article; it is included only to show how each viewer handles very large data. Three figures stream OME-Zarr data from cloud object storage to Vizarr, microATLAS and Find Nuclei, while the fourth streams a smaller Deep Zoom (DZI) subset from GitHub Pages to OpenSeadragon. Each viewer is embedded with a single MyST directive, shown below its figure. -For Vizarr and OpenSeadragon, authors replace the source URL with a link to their own data, while microATLAS and Find Nuclei generate the embedding code for a chosen view, so adding an interactive figure amounts to pasting a short block of markup. +For Vizarr and OpenSeadragon, authors replace the source URL with a link to their own data, while microATLAS and Find Nuclei generate the embedding code, so adding an interactive figure amounts to pasting a block of markup. ## OME-Zarr From c5902698ac5f6f0c0a33f4a21e2d468f82d0740a Mon Sep 17 00:00:00 2001 From: RussellBarkley Date: Thu, 29 Oct 2026 19:30:07 -0400 Subject: [PATCH 15/18] Update 02_approach.md --- 02_approach.md | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/02_approach.md b/02_approach.md index 9b48e697..fe14d013 100644 --- a/02_approach.md +++ b/02_approach.md @@ -23,8 +23,8 @@ Authors can also build custom viewers and embed them within their online article Brodrick developed [microATLAS](https://github.com/LadInTheLab/microATLAS-widget) to present the large multiplexed immunofluorescence datasets in this article, and its [widget builder](https://ladinthelab.github.io/microATLAS-widget/builder.html) generates embedding code that specifies both the image and its display settings. We also collaborated with the developers of [Find Nuclei](https://www.find-nuclei.com/), a browser-based dashboard for OME-Zarr datasets, so that its toolbar embed button generates MyST code for embedding the viewer in Elemental Microscopy articles [@FindNuclei2026]. -The four figures below are interactive microscopy maps for readers to try, each showing the same demonstration dataset: a mosaic of roughly one million nucleus images [@doi:10.5281/zenodo.18776682]. -This data is not analyzed in this article; it is included only to show how each viewer handles very large data. +The four figures below are interactive microscopy maps for readers to try, each showing the same demo dataset: a mosaic of around one million nucleus images [@doi:10.5281/zenodo.18776682]. +This data is not analyzed in this article; it is included only to show how each viewer handles very large images. Three figures stream OME-Zarr data from cloud object storage to Vizarr, microATLAS and Find Nuclei, while the fourth streams a smaller Deep Zoom (DZI) subset from GitHub Pages to OpenSeadragon. Each viewer is embedded with a single MyST directive, shown below its figure. For Vizarr and OpenSeadragon, authors replace the source URL with a link to their own data, while microATLAS and Find Nuclei generate the embedding code, so adding an interactive figure amounts to pasting a block of markup. From f5cb3a8e28ecb6465535e133277393f2504dbf1a Mon Sep 17 00:00:00 2001 From: RussellBarkley Date: Fri, 30 Oct 2026 13:09:28 -0400 Subject: [PATCH 16/18] Update 02_approach.md --- 02_approach.md | 19 +++++++++---------- 1 file changed, 9 insertions(+), 10 deletions(-) diff --git a/02_approach.md b/02_approach.md index fe14d013..e0cc3e04 100644 --- a/02_approach.md +++ b/02_approach.md @@ -10,7 +10,7 @@ Free and open-source solutions [@doi:10.1242/jcs.262198] and recent advances in Most journals publish articles as static pages that cannot run code, so interactive figures must be provided as links to external pages. Even [Elsevier's Virtual Microscope](https://www-prod.elsevier.com/researcher/author/tools-and-resources/data-visualization/virtual-microscope) is opened from links in figure captions. To our knowledge, Elemental Microscopy is among the first journals that allows interactive viewers to be embedded directly within the article, so each figure is a live view of the full-resolution dataset rather than a static rendering. -Here we describe a workflow for this kind of virtual microscopy: datasets are acquired automatically, converted to multi-scale [pyramid]() formats, hosted in the cloud, and streamed to viewers embedded in a paper ([](#abstract)). +Here we describe a workflow for this kind of virtual microscopy: datasets are acquired automatically, converted to multi-scale [pyramid]() formats, hosted in the cloud, and streamed to viewers embedded in an article ([](#abstract)). ```{figure} ./figures/Virtual_microscopy.png :label: abstract @@ -18,13 +18,12 @@ Virtual microscopy. 1. Automated dataset collection with any suitable microscope ``` Elemental Microscopy natively supports two interactive viewers; [Vizarr](https://github.com/hms-dbmi/vizarr) [@doi:10.1038/s41592-022-01482-7] and [OpenSeadragon](https://openseadragon.github.io/), which enable virtual microscopy of OME-Zarr and Deep Zoom images, respectively. -To use either viewer, authors copy the provided markdown and replace the source URL with a link to their own data. -Authors can also build custom viewers and embed them within their online articles. -Brodrick developed [microATLAS](https://github.com/LadInTheLab/microATLAS-widget) to present the large multiplexed immunofluorescence datasets in this article, and its [widget builder](https://ladinthelab.github.io/microATLAS-widget/builder.html) generates embedding code that specifies both the image and its display settings. -We also collaborated with the developers of [Find Nuclei](https://www.find-nuclei.com/), a browser-based dashboard for OME-Zarr datasets, so that its toolbar embed button generates MyST code for embedding the viewer in Elemental Microscopy articles [@FindNuclei2026]. +Authors can also build custom viewers. +Brodrick developed [microATLAS](https://github.com/LadInTheLab/microATLAS-widget) to present the multiplexed immunofluorescence imaging datasets in this article, and its [widget builder](https://ladinthelab.github.io/microATLAS-widget/builder.html) generates embedding code that specifies both the image and its display settings. +We also collaborated with the developers of [Find Nuclei](https://www.find-nuclei.com/), a browser-based dashboard for OME-Zarr datasets, so that its toolbar generates MyST code for embedding the viewer in Elemental Microscopy articles [@FindNuclei2026]. -The four figures below are interactive microscopy maps for readers to try, each showing the same demo dataset: a mosaic of around one million nucleus images [@doi:10.5281/zenodo.18776682]. -This data is not analyzed in this article; it is included only to show how each viewer handles very large images. +The four figures below are interactive microscopy maps for readers to try, each using the same dataset: a mosaic of roughly one million nucleus images [@doi:10.5281/zenodo.18776682]. +This data was not analyzed in this article; it was included only to show how each viewer handles a very large image. Three figures stream OME-Zarr data from cloud object storage to Vizarr, microATLAS and Find Nuclei, while the fourth streams a smaller Deep Zoom (DZI) subset from GitHub Pages to OpenSeadragon. Each viewer is embedded with a single MyST directive, shown below its figure. For Vizarr and OpenSeadragon, authors replace the source URL with a link to their own data, while microATLAS and Find Nuclei generate the embedding code, so adding an interactive figure amounts to pasting a block of markup. @@ -44,7 +43,7 @@ As an advanced implementation of microscopy maps [@doi:10.1242/jcs.262198], pyra ```{code} markdown :label: vizarr_code -:caption: Minimal markdown to embed Vizarr in Elemental Microscopy. Replace the source with your data. +:caption: Example markdown to embed Vizarr. Replace the source with your data. :::{any:bundle} https://curvenote.github.io/widgets/widgets/vizarr-viewer.js { "source": "https://nyu1.osn.mghpcc.org/barkley-replication/nuclei_mosaic.zarr", @@ -97,7 +96,7 @@ As an advanced implementation of microscopy maps [@doi:10.1242/jcs.262198], pyra ```{code} markdown :label: microatlas_code -:caption: Example markdown to embed microATLAS in Elemental Microscopy. Create your own with the [builder](https://ladinthelab.github.io/microATLAS-widget/builder.html). +:caption: Example markdown to embed microATLAS. Create your own with the [builder](https://ladinthelab.github.io/microATLAS-widget/builder.html). :::{any:bundle} https://LadInTheLab.github.io/microATLAS-widget/widget.js { "source": "https://nyu1.osn.mghpcc.org/barkley-replication/nuclei_mosaic.zarr", @@ -121,7 +120,7 @@ As an advanced implementation of microscopy maps [@doi:10.1242/jcs.262198], pyra ```{code} markdown :label: findnuclei_code -:caption: Example markdown to embed [Find Nuclei](https://www.find-nuclei.com/) in Elemental Microscopy [@FindNuclei2026]. +:caption: Example markdown to embed Find Nuclei [@FindNuclei2026]. Create your own with the [viewer](https://find-nuclei.github.io/). :::{any:bundle} https://find-nuclei.github.io/embed/v1/widget.mjs { "url": "https://nyu1.osn.mghpcc.org/barkley-replication/nuclei_mosaic.zarr", From 86c94e53b1086704147aef2d01590009293215c2 Mon Sep 17 00:00:00 2001 From: RussellBarkley Date: Fri, 30 Oct 2026 13:13:00 -0400 Subject: [PATCH 17/18] Update 02_approach.md --- 02_approach.md | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/02_approach.md b/02_approach.md index e0cc3e04..21299e02 100644 --- a/02_approach.md +++ b/02_approach.md @@ -17,9 +17,9 @@ Here we describe a workflow for this kind of virtual microscopy: datasets are ac Virtual microscopy. 1. Automated dataset collection with any suitable microscope. ZDC: Z-drift compensation. 2. Stitch tiles then convert the image to DZI or OME-Zarr, host online. 3. Image tiles or data chunks are retrieved from cloud storage as readers interact with microscopy maps. ``` -Elemental Microscopy natively supports two interactive viewers; [Vizarr](https://github.com/hms-dbmi/vizarr) [@doi:10.1038/s41592-022-01482-7] and [OpenSeadragon](https://openseadragon.github.io/), which enable virtual microscopy of OME-Zarr and Deep Zoom images, respectively. +Elemental Microscopy natively supports two interactive viewers; [Vizarr](https://github.com/hms-dbmi/vizarr) [@doi:10.1038/s41592-022-01482-7] and [OpenSeadragon](https://openseadragon.github.io/), which enable virtual microscopy of OME-Zarr and Deep Zoom images. Authors can also build custom viewers. -Brodrick developed [microATLAS](https://github.com/LadInTheLab/microATLAS-widget) to present the multiplexed immunofluorescence imaging datasets in this article, and its [widget builder](https://ladinthelab.github.io/microATLAS-widget/builder.html) generates embedding code that specifies both the image and its display settings. +Brodrick developed [microATLAS](https://github.com/LadInTheLab/microATLAS-widget) to present the multiplexed immunofluorescence OME-Zarr datasets in this article, and its [widget builder](https://ladinthelab.github.io/microATLAS-widget/builder.html) generates embedding code that specifies both the image and its display settings. We also collaborated with the developers of [Find Nuclei](https://www.find-nuclei.com/), a browser-based dashboard for OME-Zarr datasets, so that its toolbar generates MyST code for embedding the viewer in Elemental Microscopy articles [@FindNuclei2026]. The four figures below are interactive microscopy maps for readers to try, each using the same dataset: a mosaic of roughly one million nucleus images [@doi:10.5281/zenodo.18776682]. From efba179de01b32695b640d8b4f82d1a727e5abee Mon Sep 17 00:00:00 2001 From: RussellBarkley Date: Fri, 30 Oct 2026 13:27:04 -0400 Subject: [PATCH 18/18] Update 02_approach.md --- 02_approach.md | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/02_approach.md b/02_approach.md index 21299e02..cc773537 100644 --- a/02_approach.md +++ b/02_approach.md @@ -120,7 +120,7 @@ As an advanced implementation of microscopy maps [@doi:10.1242/jcs.262198], pyra ```{code} markdown :label: findnuclei_code -:caption: Example markdown to embed Find Nuclei [@FindNuclei2026]. Create your own with the [viewer](https://find-nuclei.github.io/). +:caption: Example markdown to embed Find Nuclei. Create your own with the [viewer](https://find-nuclei.github.io/). :::{any:bundle} https://find-nuclei.github.io/embed/v1/widget.mjs { "url": "https://nyu1.osn.mghpcc.org/barkley-replication/nuclei_mosaic.zarr", @@ -148,7 +148,7 @@ By default, readers cannot control dimensions like channels or time, so it is be ```{code} markdown :label: openseadragon_code -:caption: Minimal markdown to embed OpenSeadragon in Elemental Microscopy. Replace the source with your DZI. +:caption: Example markdown to embed OpenSeadragon. Replace the source with your DZI. :::{any:bundle} https://curvenote.github.io/widgets/widgets/openseadragon.mjs { "tileSources": "https://russellbarkley.github.io/nucleusnet-10k/nucleusnet_10k.dzi"