Understanding Liposome Behaviour in Hydrogel Matrices

Ojaswita Pant; Manuel Bibrowski

Interactive viewers

Per-well microscopy for GFP expression in hydrogels, as interactive viewers. The well descriptions are on the main page, under Results.

The viewers are stacked rather than tabbed. The Vizarr widget creates its viewer on a detached element with no width. It never re-measures. Any instance hidden when the page mounts renders blank permanently.

Each viewer sets "menuOpen": true, because the widget starts its sidebar closed by default and that sidebar holds the per-channel contrast sliders a reader needs.

Changed on 2026-10-12: the viewers now point at ../../plugins/vizarr/vizarr-viewer.mjs, not at the widget on curvenote.github.io. myst-theme mounts an anywidget inside a shadow root. The style tags Material-UI and vizarr inject into document.head do not cross that boundary. With the upstream widget, the sidebar renders with its labels but zero-sized sliders. An earlier screenshot of this page showed thin vertical bars where the Z and channel sliders belong, for that reason. The local copy mirrors those styles into the shadow root, the same fix already in place for the pH-sensor DevNote’s viewers. This page’s two prior reconciliations settled on the upstream widget instead, because the local copy then on hand failed curvenote check. That copy is not this one: plugins/vizarr/ is a later, shared fix, and it passes.

These viewers do not survive JATS conversion. The archived record of this result, once one exists, is a static figure and the prose on the main page, not an image here.

Both stores are live, and the 2026-10-11 404s were a v2 check against a v3 store

RESOLVED on 2026-10-12. Both stores answer at zarr.json, with 200. The 2026-10-11 check tested .zattrs, .zgroup and .zarray, the Zarr v2 marker names. Both stores are Zarr v3. A Zarr v3 store uses zarr.json for its group and array markers instead. Every path tried on 2026-10-11 answered 404 for that reason, even though the data was already there. A pixel chunk fetched directly from E/12/0/s0/c/0/0/0/0/0 also returns 200. The image data itself, not only the metadata, is reachable.

https://data.nucleus.engineering/microscopy/nucleus-bnext-01/OP-20261006_endpoint-vescile-gel-MB_2026-10-06_12-23-15.511547.zarr
https://data.nucleus.engineering/microscopy/nucleus-bnext-01/OP-20261006_endpoint-vescile-gel-MB-zstack-E15_2026-10-06_12-58-55.990402.zarr

Each store’s zarr.json carries an OME-NGFF plate record. That record states the well lists read earlier from the .parquet companions. The “E12” store is a 4-row (D, E, F, G), 1-column (12) plate. All four wells, including G12, exist as groups in the store. The “E15” store is a 4-row, 4-column (14, 15, 16, 21) plate. All sixteen wells exist. The well paths below, <row>/<column>/0, are checked against this record, not inferred from the .parquet alone as they were on 2026-10-11.

Each well’s image group carries two channels, Brightfield and GFP, and a multiscale pyramid with levels s0 through s4. The viewers below render against that data directly.

E12 — GFP-GUVs+LUVs in solution¶

[zarr-viewer, source:https://data.nucleus.engineering/microscopy/nucleus-bnext-01/OP-20261006_endpoint-vescile-gel-MB_2026-10-06_12-23-15.511547.zarr/E/12/0, caption: (GFP-GUVs+LUVs in solution, well E12.)]

G12 — outer-solution-only control¶

[zarr-viewer, source:https://data.nucleus.engineering/microscopy/nucleus-bnext-01/OP-20261006_endpoint-vescile-gel-MB_2026-10-06_12-23-15.511547.zarr/G/12/0, caption: (Outer-solution-only control, well G12.)]

G12 exists in the store, and carries no segmented objects in the parquet table

Narrowed on 2026-10-12. The store’s own zarr.json lists G12 as a well group, alongside D12, E12 and F12. The well is not missing from the store. Its absence is only from the .parquet, the per-object segmentation table. G12 is the outer-solution-only control, so an empty segmentation table for it is the expected result, not a gap in the data.

E14 — GFP-GUVs+LUVs in PEG4Nb pre-gel¶

[zarr-viewer, source:https://data.nucleus.engineering/microscopy/nucleus-bnext-01/OP-20261006_endpoint-vescile-gel-MB-zstack-E15_2026-10-06_12-58-55.990402.zarr/E/14/0, caption: (GFP-GUVs+LUVs in PEG4Nb pre-gel, well E14.)]

E15 — GFP-GUVs+LUVs in ULGA, z-stack¶

[zarr-viewer, source:https://data.nucleus.engineering/microscopy/nucleus-bnext-01/OP-20261006_endpoint-vescile-gel-MB-zstack-E15_2026-10-06_12-58-55.990402.zarr/E/15/0, caption: (GFP-GUVs+LUVs in ULGA, well E15, z-stack.)]

E16 — GFP-GUVs+LUVs in LGA¶

[zarr-viewer, source:https://data.nucleus.engineering/microscopy/nucleus-bnext-01/OP-20261006_endpoint-vescile-gel-MB-zstack-E15_2026-10-06_12-58-55.990402.zarr/E/16/0, caption: (GFP-GUVs+LUVs in LGA, well E16.)]

E21 — GFP-GUVs+LUVs in PEG4Nb gel¶

[zarr-viewer, source:https://data.nucleus.engineering/microscopy/nucleus-bnext-01/OP-20261006_endpoint-vescile-gel-MB-zstack-E15_2026-10-06_12-58-55.990402.zarr/E/21/0, caption: (GFP-GUVs+LUVs in PEG4Nb gel, well E21.)]