CryoNAV Interface Tour: Difference between revisions
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Clicking a grid opens its detail page: acquisition parameters (voltage, pixel size, camera, dose, tilt range, software, operator), per-grid tags and notes, and a tabular list of all tilt series collected on that grid with status, user rating, tags and processing state. The page also exposes the '''SearchMaps''' sub-tab for browsing the medium-magnification overviews and the spatial overlay of tilt series on them; see [[CryoNAV Grid Visualization Tools|Grid Visualization]] for atlas, search-map overlay, card view and list view. | Clicking a grid opens its detail page: acquisition parameters (voltage, pixel size, camera, dose, tilt range, software, operator), per-grid tags and notes, and a tabular list of all tilt series collected on that grid with status, user rating, tags and processing state. The page also exposes the '''SearchMaps''' sub-tab for browsing the medium-magnification overviews and the spatial overlay of tilt series on them; see [[CryoNAV Grid Visualization Tools|Grid Visualization]] for atlas, search-map overlay, card view and list view. | ||
== Tilt series == | |||
[[File:CryoNAV tilt series detail.png|center|thumb|800px|Tilt series detail page: acquisition metadata, star rating, tags, current processing branch, processing history, and image gallery (raw, aligned, CTF, defocus).]] | |||
Each tilt series has a detail page accessible from the grid view. It shows acquisition metadata (dose, tilt count, tilt range and increment, defocus, voltage, magnification, pixel size, camera, spherical aberration, image dimensions), user-assigned rating and tags, the currently-selected processing branch (with step progress, e.g. ''Alt CTF Step 11/13''), processing history, and an image gallery with thumbnails for the raw, aligned, CTF, and defocus views. Buttons jump to the SearchMap (spatial context) or to the Pipeline. | |||
== Pipeline == | |||
[[File:CryoNAV pipeline.png|center|thumb|800px|Pipeline view for a single tilt series: catalog steps rendered as a DAG with status colors, branches drawn side by side, right panel exposes parameters for the selected step.]] | |||
The Pipeline is the per-tilt-series processing canvas. It renders the full chain of catalog modules (motion correction, X-ray removal, coarse alignment, tracking, bead/seed models, fine alignment, aligned stack, sample tomogram, positioning, CTF correction, reconstruction, denoising) as a DAG with status colors. Forks are drawn side by side: in the example, a second branch ''Branch AAA'' forked from the Bead/Seed Models step shows alternative downstream choices for direct comparison (see [[CryoNAV Key Concepts#Immutable processing branches|Immutable processing branches]]). The right panel exposes the parameter form for the selected step, plus Job / Logs and Outputs tabs. A workflow can be applied to the chain from the top centre. | |||
== Jobs == | == Jobs == | ||
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The Jobs page shows running, completed and failed processing jobs across all projects the user can see. Each row gives job type (motion correction, alignment, CTF, reconstruction, denoising, ...), status, run time and links into the relevant tilt series or run record. | The Jobs page shows running, completed and failed processing jobs across all projects the user can see. Each row gives job type (motion correction, alignment, CTF, reconstruction, denoising, ...), status, run time and links into the relevant tilt series or run record. | ||
== Tags == | |||
[[File:CryoNAV tags.png|center|thumb|800px|Tag management with scope, usage count and creator.]] | |||
The Tags page is the central registry of tags used across the deployment. Each row shows the tag name (with its display color), description, scope (Tilt Series, Grid, Search Map, Project, or combinations), creator and creation date, and the current usage count. Tags can be filtered by scope and by ownership ('''Mine''' vs '''All'''). See [[CryoNAV Sample Experiment Management|Sample & Experiment Mgt.]] for how tags are applied during curation. | |||
== Storage == | == Storage == | ||
[[File:CryoNAV storage.png|center|thumb|800px|Storage | The Storage page has two tabs. | ||
[[File:CryoNAV storage overview.png|center|thumb|800px|Storage / Overview tab: per-project disk usage breakdown.]] | |||
'''Overview''' summarises disk usage per project, broken down into raw data, intermediate processing files, and final outputs. | |||
[[File:CryoNAV storage cleanup.png|center|thumb|820px|Storage / Cleanup tab: select intermediate files to delete while preserving raw data and processing records.]] | |||
'''Cleanup''' lets the user selectively delete intermediate files from superseded processing branches while retaining the raw frames and the database record. Because every processing step's parameters are stored, deleted intermediates can be regenerated from raw data at any time. See [[CryoNAV Data Storage Backup|Data Storage & Backup]] for the full discussion. | |||
== Export == | |||
[[File:CryoNAV export.png|center|thumb|800px|Export builder for reports, tabular data and ZIP bundles.]] | |||
The Export page is the entry point for generating reports (Create Report), tabular exports (Excel and CSV), and configurable ZIP bundles containing selected processed outputs and the parameters needed to reproduce them. See [[CryoNAV Data Sharing Archiving|Data Sharing & Archiving]] for the export contents. | |||
== Settings == | |||
[[File:CryoNAV settings.png|center|thumb|800px|User settings.]] | |||
The Settings page exposes per-user preferences (display, notifications, default project, etc.). System-wide configuration lives in the Admin section. | |||
== Admin: Users == | |||
[[File:CryoNAV admin users.png|center|thumb|800px|User administration (admin only).]] | |||
System administrators manage user accounts here: create users, assign global roles (System Administrator, Editor, Viewer), and audit activity. | |||
== Admin: Compute backends == | == Admin: Compute backends == | ||
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System administrators configure the available compute backends -- typically one or more SLURM partitions and a local-workstation backend. At job submission time the user picks which backend to run on; see [[CryoNAV Overview Tomogram Processing#Local and HPC execution|Local and HPC execution]] for the dual-mode design. | System administrators configure the available compute backends -- typically one or more SLURM partitions and a local-workstation backend. At job submission time the user picks which backend to run on; see [[CryoNAV Overview Tomogram Processing#Local and HPC execution|Local and HPC execution]] for the dual-mode design. | ||
== Admin: Monitoring == | |||
[[File:CryoNAV admin monitoring.png|center|thumb|800px|System monitoring (admin only).]] | |||
Live status of CryoNAV's services, compute backends, and job queues. Used by administrators to spot stalled jobs, overloaded partitions, or failed services. | |||
== Admin: Backup == | |||
[[File:CryoNAV admin backup.png|center|thumb|800px|Backup management (admin only).]] | |||
Administrators schedule and trigger backups of the SQLite database and configure backup retention. The image storage on the filesystem is backed up separately by the host's standard backup mechanism. | |||
== See also == | == See also == | ||
Latest revision as of 23:57, 20 May 2026
A quick visual tour of the CryoNAV web interface. Screenshots are taken from an in-development build with mock data; labels and exact layouts may change before release.
Dashboard
The dashboard is the landing page after login. It shows the user's most recently active projects as cards (with tilt-series count and storage footprint) and a table of the most recent processing jobs across all projects.
Projects
The full project list, with owner, tilt-series count, and storage. Projects are the unit of access control (see Key Concepts). The New Project button creates an empty project that grids can then be imported into.
Clicking a project opens its detail page: tabs for Overview, Grids, and Jobs; the right-hand pane lists members and their roles. Tags can be added to projects and tilt series for filtering and reporting.
Grids
The Grids tab lists the physical EM grids attached to the project, in the order they were imported via SmartScan.
Clicking a grid opens its detail page: acquisition parameters (voltage, pixel size, camera, dose, tilt range, software, operator), per-grid tags and notes, and a tabular list of all tilt series collected on that grid with status, user rating, tags and processing state. The page also exposes the SearchMaps sub-tab for browsing the medium-magnification overviews and the spatial overlay of tilt series on them; see Grid Visualization for atlas, search-map overlay, card view and list view.
Tilt series
Each tilt series has a detail page accessible from the grid view. It shows acquisition metadata (dose, tilt count, tilt range and increment, defocus, voltage, magnification, pixel size, camera, spherical aberration, image dimensions), user-assigned rating and tags, the currently-selected processing branch (with step progress, e.g. Alt CTF Step 11/13), processing history, and an image gallery with thumbnails for the raw, aligned, CTF, and defocus views. Buttons jump to the SearchMap (spatial context) or to the Pipeline.
Pipeline
The Pipeline is the per-tilt-series processing canvas. It renders the full chain of catalog modules (motion correction, X-ray removal, coarse alignment, tracking, bead/seed models, fine alignment, aligned stack, sample tomogram, positioning, CTF correction, reconstruction, denoising) as a DAG with status colors. Forks are drawn side by side: in the example, a second branch Branch AAA forked from the Bead/Seed Models step shows alternative downstream choices for direct comparison (see Immutable processing branches). The right panel exposes the parameter form for the selected step, plus Job / Logs and Outputs tabs. A workflow can be applied to the chain from the top centre.
Jobs
The Jobs page shows running, completed and failed processing jobs across all projects the user can see. Each row gives job type (motion correction, alignment, CTF, reconstruction, denoising, ...), status, run time and links into the relevant tilt series or run record.
Tags
The Tags page is the central registry of tags used across the deployment. Each row shows the tag name (with its display color), description, scope (Tilt Series, Grid, Search Map, Project, or combinations), creator and creation date, and the current usage count. Tags can be filtered by scope and by ownership (Mine vs All). See Sample & Experiment Mgt. for how tags are applied during curation.
Storage
The Storage page has two tabs.
Overview summarises disk usage per project, broken down into raw data, intermediate processing files, and final outputs.
Cleanup lets the user selectively delete intermediate files from superseded processing branches while retaining the raw frames and the database record. Because every processing step's parameters are stored, deleted intermediates can be regenerated from raw data at any time. See Data Storage & Backup for the full discussion.
Export
The Export page is the entry point for generating reports (Create Report), tabular exports (Excel and CSV), and configurable ZIP bundles containing selected processed outputs and the parameters needed to reproduce them. See Data Sharing & Archiving for the export contents.
Settings
The Settings page exposes per-user preferences (display, notifications, default project, etc.). System-wide configuration lives in the Admin section.
Admin: Users
System administrators manage user accounts here: create users, assign global roles (System Administrator, Editor, Viewer), and audit activity.
Admin: Compute backends
System administrators configure the available compute backends -- typically one or more SLURM partitions and a local-workstation backend. At job submission time the user picks which backend to run on; see Local and HPC execution for the dual-mode design.
Admin: Monitoring
Live status of CryoNAV's services, compute backends, and job queues. Used by administrators to spot stalled jobs, overloaded partitions, or failed services.
Admin: Backup
Administrators schedule and trigger backups of the SQLite database and configure backup retention. The image storage on the filesystem is backed up separately by the host's standard backup mechanism.