Help & Guide

Getting Oriented

MorphoTyper and Stats Browser are separate apps with different goals.

MorphoTyper: Use /ew2/morpho_typer for filtering, skeleton previews, coverage review, Neuroglancer inspection, proofreading notes, 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.

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.

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

Pagination controls: Rows / page defaults to 10 so previews stay responsive; Prev/Next moves through the fetched segment IDs.
Row selection: Click a row to set it as the active cell, populate Selected Cell Stats, update the coverage/stratification selection markers, and prepare 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.

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.

Use the review cards below Selected Cell Stats when you are ready to inspect or annotate a specific cell.

Neuroglancer view: The Neuroglancer card starts collapsed. Open the card to load the viewer URL; Open Viewer becomes active after the card is open and a URL is available.
Needs Proofreading / Add Notes: The notes card starts collapsed. Open it to edit User Name, User Email ID, Cell Class, Cell Type (Human), Needs Proofreading, and Add Notes for the selected segment.
Submit notes: Submit appends the selected segment_id, user details, labels, proofreading flag, notes, and a timezone-aware timestamp to proofreading_and_notes/proofreading_and_notes.csv in GCS.
Export All Found Stats: Use the Selected Cell Stats header to choose CSV, Pickle, MAT, or HDF5 and export arbor statistics for all fetched segment IDs. The export stays active whether the card is collapsed or open.

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. Population stats and coverage are available when all skeletons are loaded.
Coverage plot: Red crosses mark soma positions. Clicking directly on a red cross selects that segment, scrolls the Skeletons table to its row, and shows a dark-orange selected cross with a white boundary. The first segment is selected by default after a fresh search.
Stratification Profiles: Each heatmap row corresponds to a segment ID. Clicking a row selects that segment, scrolls to the matching Skeletons row, and outlines the heatmap row with dark orange and a white boundary.
Selected Cell stats: After selecting a row, single-cell metrics populate for fast comparisons. Export controls live in the Selected Cell Stats title bar.
Stratification export: The Stratification Profiles Export button stays inactive until a plot has loaded.

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.

Tips for keeping the UI responsive and data current.

Slow previews: Use Cancel Process, narrow filters, keep Rows / page near the 10-row default, or avoid Load All Skeletons unless you need population coverage.
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.

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.
Use coverage crosses or stratification heatmap rows to select cells and jump to the matching Skeletons row.
Open Neuroglancer, submit proofreading notes, or export all found stats when you are ready to analyze.
Use Stats Browser to build Scatter/Bar/Intersection plots and save PNGs.

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

If you see unexpected behavior, capture a screenshot, note the selected segment ID, and refresh the Google Sheet cache before reporting the issue.