ETSAM Plugin for napari

The napari-etsam plugin runs ETSAM inside napari, a free image viewer for multi-dimensional data. You open a tomogram, install and activate plugin, click Segment membranes. The membrane mask appears as an new label layer that you can refine, inspect and save.

Note On first start, if ETSAM is missing, click Install ETSAM to set it up in its own environment (or install it beforehand using the ETSAM installer).

ETSAM membrane mask (yellow) on EMD-4949 in napari, with the ETSAM panel on the right.

Requirements

Installation

1. Install the plugin

From napari (recommended):

1. Install napari if you don't have it yet. The napari bundle is the easiest option.
2. In napari, open Plugins ▸ Install/Uninstall Plugins….
3. Search for ETSAM, click Install next to napari-etsam, and restart napari.

With pip, in napari's Python environment:

pip install napari-etsam

Tip To install the plugin from a checkout of the ETSAM repository instead, use the Python of napari's environment:

/path/to/napari/python -m pip install ./ETSAM/external_plugins/napari-etsam

2. First start: click Install ETSAM

ETSAM itself runs in its own environment, separate from napari. When you open the ETSAM panel, the plugin checks whether ETSAM is installed. If it is missing on a supported computer, the panel shows an Install ETSAM button. Click it to start the ETSAM installer. Opening the panel does not start an installation.

Installation downloads about 5 GB and may take 10–15 minutes. Keep napari open until it finishes; the panel shows progress. The installer puts ETSAM into ~/etsam_env (on Windows, %USERPROFILE%\etsam_env). Subsequent use starts immediately.

ETSAM requires Linux or Windows and an NVIDIA GPU. macOS is not supported. Contributions are welcome to extend hardware/software support.

Segmenting a Tomogram

1. Open the panel: Plugins ▸ ETSAM Membrane Segmentation (napari-etsam).
2. Open a tomogram: drag and drop an .mrc file onto napari, or click Open… in the panel. The new layer is selected as the Tomogram automatically.
3. Optionally, tick Clean up mask or Closely spaced membranes (see Options).
4. Click Segment membranes. The progress bar follows ETSAM through Stage 1 and Stage 2 slice by slice, then through clean-up. Click Cancel to stop at any time.

Progress is reported per slice for each stage, with an estimate of the time remaining.

5. When finished, a <tomogram> membranes label layer is added on top of the tomogram, and the panel shows the run time and the fraction of voxels classified as membrane.
6. Refine: move the Threshold slider. The mask updates instantly, and clean-up is re-applied in the background if enabled. Lower values find more (and fainter) membrane; higher values give fewer false positives. Reset returns to the default -0.25. You can also correct the mask by hand with napari's label tools (paint, erase, fill).
7. Save: click Save mask… (the mask at the current threshold, including manual edits) or Save logits… (raw membrane scores). Files are written as .mrc with the tomogram's voxel size, so they overlay directly in ChimeraX, IMOD or other tools. File ▸ Save Selected Layers… with a .mrc file name works too.

Options

The main options are in the panel. The rest are under Advanced settings.

The plugin and the etsam command produce the same results for the same settings.

Troubleshooting

When something goes wrong, the panel shows a red box with the problem and a suggested fix. Show details displays the full error, and Copy error report copies it with your system information (versions, GPU) for a GitHub issue.

Uninstalling

Remove the plugin with Plugins ▸ Install/Uninstall Plugins ▸ napari-etsam ▸ Uninstall, or pip uninstall napari-etsam. To remove ETSAM completely, refer uninstall section in Installation guide.

Cite:

Selvaraj, J., Cheng, J. ETSAM: effectively segmenting cell membranes in cryo-electron tomograms. Nat Commun (2026). https://doi.org/10.1038/s41467-026-77962-7