Adding another viewer

02_approach.md

@@ -5,21 +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.
-Our approach combined automated image acquisition, multi-scale [pyramid](<wiki:Pyramid_(image_processing)>) formats and embedded interactive viewers ([](#abstract)).
+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](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](<wiki:Pyramid_(image_processing)>) formats, hosted in the cloud, and streamed to viewers embedded in an 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. 
-All three viewers are readily 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.
+Authors can also build custom viewers.
+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].
+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.
 
 ## OME-Zarr
 
@@ -30,45 +37,99 @@ As an advanced implementation of microscopy maps [@doi:10.1242/jcs.262198], pyra
 
 ### 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%
+```
+
 ```{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://your-bucket.s3.amazonaws.com/sample.zarr/",
+  "source": "https://nyu1.osn.mghpcc.org/barkley-replication/nuclei_mosaic.zarr",
   "height": "600px"
 }
 :::
 ```
 
 ### microATLAS
 
-```{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
+:::{any:bundle} https://LadInTheLab.github.io/microATLAS-widget/widget.js
 {
-  "source": "https://your-bucket.s3.amazonaws.com/sample.zarr/",
+  "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" }
+  ]
+}
+:::
+
+```{code} markdown
+:label: microatlas_code
+: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",
+  "width": "600px",
+  "height": "600px"
 }
 :::
 ```
 
-```{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
+
+:::{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": "600",
+  "invert": true
+}
+:::
+
+```{code} markdown
+:label: findnuclei_code
+: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",
+  "channels": "0:on:FFFFFF:0:240",
+  "x": 2115, "y": 1688, "zoom": -1.9,
+  "height": "600",
+  "invert": true
+}
+:::
 ```
 
 ## Deep Zoom
@@ -79,18 +140,18 @@ By default, readers cannot control dimensions like channels or time, so it is be
 
 ### OpenSeadragon
 
+:::{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.
+:caption: Example markdown to embed OpenSeadragon. Replace the source with your DZI.
 :::{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"
 }
 :::
 ```
-
-## 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.

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.

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},
+}