Visualization (CryoSiam‑Vis)¶
The cryosiam-vis package provides interactive visualization utilities (via napari and dash) for inspecting results produced by CryoSiam:
- Denoised tomograms
- Semantic segmentation results
- Instance segmentation results (including filtered instances)
- Particle/coordinate sets from .star or .csv files
- Subtomogram embedding spaces (UMAP / clustering)
Most visualization commands open an interactive napari viewer, while embedding exploration uses a lightweight dash interface.
Install¶
Refer to the CryoSiam‑Vis installation guide.
Command overview¶
All visualizations are accessed through a single CLI with subcommands:
cryosiam_vis --version
cryosiam_vis <subcommand> [arguments]
Important: All visualization commands reuse the same configuration files used during CryoSiam inference. No separate visualization configuration is required.
Available subcommands¶
visualize_denoising– visualize denoised vs raw tomogramsvisualize_semantic– overlay semantic segmentation predictionsvisualize_instance– visualize instance segmentation resultsvisualize_filtered_instance– visualize filtered instance segmentation resultsvisualize_coordinates– plot particle coordinates from.star/.csvfilesvisualize_embeddings– interactive embedding visualizationvisualize_embeddings_clusters– embedding visualization with clustering labels
visualize_denoising¶
Visualize the denoised tomogram produced by cryosiam denoise_predict and optionally compare it to the raw input.
Usage¶
cryosiam_vis visualize_denoising --config_file configs/denoise.yaml --filename TS_01.mrc
Arguments¶
| Argument | Required | Description |
|---|---|---|
--config_file |
✅ | The same YAML used with cryosiam denoise_predict. |
--filename |
✅ | Tomogram filename (including extension). |
What it loads¶
- Raw tomogram from
data_folder - Denoised tomogram from
prediction_folder - Opens both as layers in napari for side‑by‑side inspection
visualize_semantic¶
Overlay semantic segmentation predictions on the denoised tomogram.
Usage¶
cryosiam_vis visualize_semantic --config_file configs/semantic.yaml --filename TS_01.mrc
Arguments¶
| Argument | Required | Description |
|---|---|---|
--config_file |
✅ | The same YAML used with cryosiam semantic_predict. |
--filename |
✅ | Tomogram filename (including extension). |
What it loads¶
- Denoised tomogram (
data_folder) - Semantic probabilities and/or segmentation masks (
prediction_folder) - Lamella mask (if
mask_folderis defined)
visualize_instance¶
Visualize instance segmentation volumes and labels.
Usage¶
cryosiam_vis visualize_instance --config_file configs/instance.yaml --filename TS_01.mrc
Arguments¶
| Argument | Required | Description |
|---|---|---|
--config_file |
✅ | The same YAML used with cryosiam instance_predict. |
--filename |
✅ | Tomogram filename (including extension). |
What it loads¶
- Denoised tomogram (
data_folder) - Instance segmentation masks from
prediction_folder
visualize_filtered_instance¶
Visualize filtered instance segmentation results produced by cryosiam instance_filter.
Usage¶
cryosiam_vis visualize_filtered_instance --config_file configs/instance_filter.yaml --filename TS_01.mrc
Arguments¶
| Argument | Required | Description |
|---|---|---|
--config_file |
✅ | The YAML used with cryosiam instance_filter. |
--filename |
✅ | Tomogram filename (including extension). |
What it loads¶
- Denoised tomogram
- Filtered instance masks
visualize_coordinates¶
Plot particle coordinates from a .star or .csv file onto a tomogram.
Usage¶
cryosiam_vis visualize_coordinates --config_file configs/semantic_particle.yaml --filename TS_01.mrc --point_size 15
Arguments¶
| Argument | Required | Default | Description |
|---|---|---|---|
--config_file |
✅ | – | Config file used for CryoSiam particle identification |
--filename |
✅ | – | Tomogram filename (including extension) |
--point_size |
❌ | 15 |
Marker size for plotted points |
Notes¶
- Coordinates are read from the .star or .csv file specified in the configuration.
- Coordinates must be in voxel space and aligned with the tomogram.
visualize_embeddings¶
Open an interactive embedding viewer for exploratory analysis.
Usage¶
cryosiam_vis visualize_embeddings --config_file configs/subtomo_embeddings.yaml
What it does¶
- Loads embedding projections produced by the subtomogram embeddings module
- Opens an interactive dash interface for UMAP/PCA exploration
visualize_embeddings_clusters¶
Visualize embedding projections with cluster assignments.
Usage¶
cryosiam_vis visualize_embeddings_clusters --config_file configs/subtomo_embeddings.yaml --clustering kmeans
Arguments¶
| Argument | Required | Description |
|---|---|---|
--config_file |
✅ | Configuration file used for embedding generation/clustering |
--clustering |
✅ | Clustering type: kmeans or spectral |