Help & Guide

Getting Oriented

MorphoTyper and Stats Browser are separate apps with different goals.

MorphoTyper: Use /ew2/morpho_typer for filtering, skeleton previews, Neuroglancer review, and data export.
Stats Browser: Use /ew2/statsbrowser for the Stats Plot tools (scatter, bar, and intersection profiles).
Navigation: Use the top nav tabs or the home cards to jump between apps quickly.

Filtering and Search

Start by narrowing down the population you want to review.

Cell class + labels: Combine Cell Class with Human, Machine, and Other label dropdowns; all selected filters are intersected.
Other Type with symbols: Other Type filters use literal text matching, so labels that include parentheses or '+' are matched as-is.
Status and reliability: Use Status and Reliability to focus on work that is ready for review, needs help, or has a specific QC score.
Machine soma location: Filter inner, outer, or unknown machine soma zones to match coverage needs.
Segment IDs: Paste comma- or space-separated segment IDs to jump to known cells; leave blank to fetch all matches.
Search and cancel: Search loads previews and plots; Cancel Process stops in-flight work and resets the page state.
Refresh Google Sheet data: Click Refresh Google Sheet data to pull new rows and verify the Last refresh timestamp updates.

Skeleton Previews and Row Navigation

Use the Skeletons panel to browse rows and inspect previews before opening Neuroglancer.

Pagination controls: Rows / page sets how many entries draw at once; Prev/Next moves through the fetched segment IDs.
Row selection: Click a row to set it as the active cell and populate Selected Cell stats and Neuroglancer.
Row actions: Row buttons let you open interactive views and save PNGs. Save PNGs now downloads a single ZIP with skeleton + stratification images.
Download raw files: Use the row-level Download .swc & mesh.obj button to pull raw skeleton_warped_morphopy.swc and mesh.obj files for that segment.
Download all .swc files: Use the Skeletons panel Download all .swc files button to export a ZIP of SWCs for every segID in the current search.

Scale, Axes, and Visibility

Use these controls to keep morphology comparable across rows.

Lock scale across rows: Applies a consistent relative scale so each skeleton is centered and sized comparably. XY plots use equal X/Y span, and XZ uses a fixed Z range of -20 to 40.
Include axons: Toggle axon segments on/off; previews are recomputed so scale matches the current inclusion state.
Show only selected: Hides other rows so you can focus on a single cell while still keeping row controls active.

Neuroglancer and Data Export

When you are ready to inspect a specific cell, use the controls in the Neuroglancer card.

Open Viewer: Launches Neuroglancer with the current selection and camera pose.
Shorten + Copy: Creates a shareable ew2.link and copies it to your clipboard for quick reporting.
Export Data Table: Choose CSV, Pickle, MAT, or HDF5 and download arbor statistics for the fetched set.

Population, Coverage, and Selected Stats

Use population summaries to confirm whether a group matches expectations.

Population stats table: Review counts and summary metrics to confirm the filters match known cell populations.
Coverage + stratification panels: Interactive coverage (x/y) and stratification heatmaps (x/z) highlight mosaics and lamination depth.
Selected Cell stats: After selecting a row, single-cell metrics populate for fast comparisons.

Stats Browser (Stats Plot)

Use Stats Browser for deeper plots and label-based comparisons.

Plot types: Switch between Scatter, Bar, and Intersection profile plots. Axes apply to Scatter/Bar only.
Labels and legend: Filter by Human, Machine, and Other labels and toggle Show legend to manage the legend box.
Scatter plotting options: Use Plotting options to switch between points + means, means only, or points only.
Copy segIDs: Enable copying multiple segIDs and click points to build a clipboard list.
Reload and Save PNG: Reload regenerates the plot; Save PNG downloads the current view.

Troubleshooting and Performance

Tips for keeping the UI responsive and data current.

Slow previews: Use Cancel Process, narrow filters, or lower Rows / page before retrying.
Empty results: Check for mutually exclusive filters or stale sheet data.
Out-of-date info: Refresh the Google Sheet cache and confirm the Last refresh timestamp updates.

Quick start checklist

Choose MorphoTyper to review skeletons or Stats Browser to explore plots.
Set filters (cell class, labels, status, reliability) and click Search.
Review skeleton previews; use Lock scale and Include axons for consistent comparisons.
Open Neuroglancer or export the data table when you are ready to analyze.
Use Stats Browser to build Scatter/Bar/Intersection plots and save PNGs.

Need to jump in?

Open Morpho-Typer once you have read through this guide and put the tips into practice.

If you see unexpected behavior, capture a screenshot, refresh the Google Sheet cache, and share the ew2.link from the Shorten button when reporting the issue.