Workspaces

Opening…

Active

On open

Checks all files in the saved asset folders.

Assets & connection

Compatibility folder chooser

Lists the entire root, including unrelated folders. Quick reconnect requires the standard folder chooser.

Choose root folder

Selected view View name

Up to four views. Pan and zoom are linked. Click a pane to edit its channels and overlay.

Open your dataset

Choose files from your computer. Your data stays here.

AnnData Choose .h5ad Masks Choose folder Images Choose folder

Cell identity columns

ROI column Mask object ID

Navigation

Open AnnData to find your regions.

Filtering

Sorting

Order by Direction

Ordered by ROI name · ascending.

Quick jump: first X ROIs

● Unvisited ● Some views ● All views

Visits follow the current channel, contrast, normalisation and overlay settings.

Image channels

Mix up to six channels. Untick a channel to hide it.

Image normalisation

Dictionary Choose CSV / JSON

Optional Nimbus / NapariSBT dictionary. Image display only.

Fallback settings

With a dictionary loaded, unmatched channels use these settings. Minimum counts applies to all channels.

Fallback quantile (0–1) Minimum pixel counts

Cell overlay

Colour by

AppearanceOpacity

Show populations

All populations

Ctrl / Cmd-click to choose several; Shift-click for a range. No selection shows all. Representative markers requires exactly one.

Representative markers

Aligned layers

Add a folder per layer, with one image named after each ROI, or an IMC folder with channel images inside ROI subfolders. All images must share the tissue's pixel dimensions and alignment.

Layer type Name (optional) + Add layer folder

Colour: TIFF, PNG, JPEG, BMP, GIF or WebP. Scalar / labels: TIFF. IMC: TIFF channels in ROI subfolders, like Images. For labels, include label_mapping.csv or load a separate dictionary after adding the folder.

No additional layers. Their display controls appear in Views when added.

SpatialBiologyToolkit · browser viewer

Welcome to Tissue Explorer

Explore imaging mass cytometry (IMC) results, review cell populations in their tissue context, and share what you find — directly in your browser.

Follow the Guidejar tutorial

Explore your results

Compare tissue views: Up to four linked panes, six image channels per pane, and aligned histology or annotation layers.
Inspect cells and markers: Colour by population, expression or metadata. Find representative markers and compare expression curves.
Connect tissue to plots: Explore existing UMAPs and embeddings; select cells in either space. Create marker matrices, composition plots, label comparisons and alluvial plots.
Propose labels and flag cells: Rename, merge and recolour populations, add notes, and export remapping schemas or cell flags as CSV.
Pick up where you left off: Save workspaces, bookmark ROIs and positions with comments, and switch between named view presets.
Export figures: Arrange panes with calibrated scale bars and legends. Export PNG, JPEG or SVG with separate layers.

Bring these assets

For a full tissue review, choose these in Setup → Open your dataset.

AnnData .h5ad · required: Cell measurements and observations, including an ROI column and a cell ID column. Defaults: ROI and ObjectNumber.
Cell masks TIFF · for cell overlays: One labelled mask per ROI. Integer mask IDs must match AnnData cell IDs within that ROI; zero is background.
Marker images TIFF · for tissue images: One folder per ROI containing channel images. Images and masks must have the same pixel dimensions and alignment.

Folder layout & optional assets

Keep everything under one root folder so a saved workspace can reconnect to its assets. Match ROI names between AnnData, mask filenames and image folders.

MyDataset/
  cells.h5ad
  Masks/ROI_A.tiff
  Images/ROI_A/CD3.tiff
  Images/ROI_A/DNA.tiff

Optional: an image normalisation dictionary (CSV/JSON), aligned H&E or other colour images, scalar images, annotation masks with label dictionaries, and additional IMC image folders. Add these in Setup.

UMAP and other embedding coordinates must already be present in AnnData. This viewer does not compute them.

Your files stay local. AnnData, images and masks are opened read-only, including files on accessible network drives. Proposed labels, notes and flags are saved in your workspace; they do not change the source AnnData.

Ready to open a local dataset.

Review toolsHide panelShow panel

ProjectionColour byMatrixColour mapSquareOther ROIsContext limit

Current ROI · colours follow the selected view

Create a remap from an observation to begin. Source AnnData stays read only.

Select	Original population	Cells	Proposed name	Colour	Notes

Shared names merge populations; merged rows share a colour. Changes save automatically to your local workspace.

Explore your results

Bring these assets

Cell inspector