CryoNAVwiki - User contributions [en-gb]

CryoNAV Metadata Management

2026-05-20T21:57:10Z

Admin: Bot edit via cryonavedit.py: add pipeline and tilt-series detail screenshots

CryoNAV captures and manages two complementary streams of metadata: acquisition metadata extracted from microscope output files during import, and processing metadata generated during the platform's own pipeline runs.

== Acquisition metadata ==

[[File:CryoNAV tilt series detail.png|center|thumb|700px|Tilt series detail page: acquisition metadata is shown in the central panel; rating, tags, processing branch, and processing history sit on the right.]]

For each tilt series, CryoNAV stores:

* Voltage, pixel size, dose rate, camera type
* Tilt range and per-tilt angles
* Acquisition timestamps
* Stage coordinates (used for [[CryoNAV Grid Visualization Tools#Search map overlay|search map overlay]] placement)
* Search map and grid associations

This metadata is extracted automatically during [[CryoNAV Tilt Series Data Collection Import|SmartScan import]] from .mdoc files and BatchPositionsList.xml.

== Processing provenance ==

Every pipeline step's parameters are stored as individual typed fields in the database, and the complete command-line invocations are recorded. Small intermediate files (tilt angles, alignment transforms, .mdoc contents) are stored directly in the database.

This design ensures that:

* The full processing provenance is captured.
* Results can in principle be reproduced from raw data and the database record alone, even if intermediate files on disk are deleted.
* Methods sections can be reported with accurate parameter values.

See [[CryoNAV Data Storage Backup|Data Storage & Backup]] for how this enables selective intermediate-file cleanup, and [[CryoNAV Key Concepts#Immutable processing branches|Immutable processing branches]] for how parameter changes are recorded as new branches.

== Filtering and batch selection ==

Stored metadata is queryable throughout the interface. Filter expressions can combine acquisition values and user-assigned ratings/tags (see [[CryoNAV Sample Experiment Management#Rating and tagging tilt series|rating and tagging]]) for batch selection of tilt series.

== See also ==

* [[CryoNAV Tilt Series Data Collection Import|Tilt Series Data Import]]
* [[CryoNAV Data Storage Backup|Data Storage & Backup]]

[[Category:Modules]]

CryoNAV Key Concepts

2026-05-20T21:57:07Z

Admin: Bot edit via cryonavedit.py: add pipeline and tilt-series detail screenshots

Concepts that recur throughout CryoNAV's interface and workflow.

== The pipeline catalog ==

CryoNAV's processing pipeline is described by a catalog of pipeline modules (motion correction, CTF estimation, alignment, reconstruction, denoising, etc.). Each module declares its parameters and its dependencies on other modules. The same catalog drives the parameter forms in the UI, the validation rules, and the construction of command-line invocations: there is no separate template store to keep in sync.

When the user submits a step, the parameter values are supplied at submission time and recorded with the run; downstream steps are scheduled once their upstream dependencies succeed.

== Immutable processing branches ==

[[File:CryoNAV pipeline.png|center|thumb|700px|Pipeline view: the original chain (left) and an alternate ''Branch AAA'' forked from the Bead/Seed Models step (right) are drawn side by side, allowing direct comparison of parameter choices.]]

Each processing run is stored as an immutable record. Re-running a step with different parameters creates a new parallel branch rather than overwriting the original, allowing users to compare results from different parameter choices side by side. Downstream steps must be re-run on the new branch, but the original processing path remains intact.

Branches are anchored at the table and ID of the upstream step they fork from, which keeps lineage unambiguous even after intermediate files are cleaned up. Because every processing step stores its complete parameter set in the database, intermediate files can be selectively deleted to reclaim storage without losing the ability to reproduce results: the full pipeline can be re-executed from raw frames at any time.

== Curate before reconstruct ==

In a typical cryo-ET experiment, a substantial fraction of collected tilt series may be unusable due to thick ice, excessive specimen drift, contamination, or poor CTF fits. Identifying these problematic datasets early, before investing hours of compute time, saves significant resources.

CryoNAV makes curation a first-class operation within the data browsing interface, supported by automatic thumbnail generation, star ratings, tags, and combined filtering. See [[CryoNAV Grid Visualization Tools|Grid Visualization]] for the visual tools and [[CryoNAV Sample Experiment Management|Sample & Experiment Mgt.]] for tagging and rating workflows.

== Project-based collaboration ==

Projects serve as the unit of collaboration. CryoNAV's role-based access control has four levels:

* '''System Administrator''' -- manages user accounts, monitors system health, configures available computing resources.
* '''Project Owner''' -- can invite team members and assign roles. Multiple owners can be assigned per project; ownership can be transferred.
* '''Editor''' -- can submit jobs and edit project data.
* '''Viewer''' -- can browse data only.

== See also ==

* [[CryoNAV Data Lifecycle|CryoEM Data Lifecycle]]
* [[CryoNAV Sample Experiment Management|Sample & Experiment Mgt.]]

[[Category:Core Concepts]]

CryoNAV Overview Tomogram Processing

2026-05-20T21:57:05Z

Admin: Bot edit via cryonavedit.py: add pipeline and tilt-series detail screenshots

CryoNAV's processing pipeline is built around IMOD's core utilities and extended with deep-learning denoising methods. The pipeline is accessed through two complementary approaches:

* '''Per-tilt-series''' -- the interface mirrors the step-by-step workflow familiar from IMOD's eTomo: navigate to a tilt series, run a processing step, review results (thumbnails, alignment residuals, CTF plots), and proceed to the next step with adjusted parameters if needed.
* '''Batch''' -- select a batch of tilt series and submit them all for processing with a single action, applying the same parameters across the set.

[[File:CryoNAV pipeline.png|center|thumb|700px|Per-tilt-series Pipeline view: catalog steps as a DAG with status colors; a forked branch is drawn side by side. The right panel exposes parameters for the selected step.]]

== Pipeline steps ==

The processing pipeline for a typical tilt series:

* '''Motion correction''' -- correcting beam-induced specimen movement within individual tilt images.
* '''CTF estimation and correction''' -- measuring and fitting the contrast transfer function for defocus determination.
* '''Tilt series alignment''' -- aligning the tilt series using fiducial markers or patch tracking.
* '''Tomographic reconstruction''' -- computing the 3D volume via weighted back-projection or SIRT.
* '''Tomogram denoising''' (CryoCARE, DeepDeWedge) -- deep-learning denoising to improve contrast and signal-to-noise ratio. Denoising can also be applied to facility-imported data, requiring only the raw frames and reconstruction parameters.

== Job submission ==

At submission time the user selects one or more tilt series, fills in the parameter form for the chosen pipeline step (defaults come from the catalog module definition), and picks an execution backend. CryoNAV constructs the appropriate command-line invocation, records the parameter set and command alongside the run for provenance, and submits the job.

Steps can be submitted as a chain: the user selects the sequence of catalog modules to run, and each step is submitted automatically once its upstream dependencies complete. Failed steps halt the rest of the chain; downstream parameters can still be edited later before the chain is resumed.

== Local and HPC execution ==

CryoNAV supports both local workstation execution and HPC cluster submission (via SLURM) within the same deployment, and both modes are available simultaneously: a user might run a quick test alignment locally before submitting a full batch to the cluster. The execution backend is abstracted behind a common interface, so job submission, progress monitoring, log viewing, and error handling work identically regardless of where the job runs.

== Progress monitoring ==

CryoNAV provides real-time progress tracking for running jobs through two complementary strategies, adapted from the approach used by eTomo:

* '''Log parsing''' -- processing commands (both IMOD utilities and denoising tools) that print progress messages to stdout (e.g., "Processing frame 15/60" from alignframes) are parsed with regular expressions to extract the current step and total steps, yielding a percentage completion.
* '''File size monitoring''' -- for steps that produce output files of predictable size, CryoNAV monitors intermediate file growth and compares it to the expected final size derived from input metadata.

The web interface displays progress bars with smooth interpolation between server updates and human-readable ETA estimates.

== Immutable processing branches ==

Each processing run is stored as an immutable record. Re-running a step with different parameters creates a new parallel branch rather than overwriting the original, allowing side-by-side comparison of parameter choices. See [[CryoNAV Key Concepts#Immutable processing branches|Immutable processing branches]] for the full discussion.

== See also ==

* [[CryoNAV Key Concepts|Key Concepts]]
* [[CryoNAV Integration CryoEM Tools|Integration with Cryo-EM Tools]]
* [[CryoNAV Tilt Series Data Collection Import|Tilt Series Data Import]]

[[Category:Processing]]

CryoNAV Interface Tour

2026-05-20T21:57:02Z

Admin: Bot edit via cryonavedit.py: add pipeline and tilt-series detail screenshots

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 ==

[[File:CryoNAV dashboard.png|center|thumb|800px|Dashboard: recent projects (top) and recent jobs (bottom).]]

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 ==

[[File:CryoNAV projects.png|center|thumb|800px|Projects list.]]

The full project list, with owner, tilt-series count, and storage. Projects are the unit of access control (see [[CryoNAV Key Concepts|Key Concepts]]). The '''New Project''' button creates an empty project that grids can then be imported into.

[[File:CryoNAV project detail.png|center|thumb|800px|A project's overview page with members, tags, and counts.]]

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 ==

[[File:CryoNAV grids.png|center|thumb|800px|Project grids tab.]]

The Grids tab lists the physical EM grids attached to the project, in the order they were imported via [[CryoNAV Tilt Series Data Collection Import|SmartScan]].

[[File:CryoNAV grid detail.png|center|thumb|800px|Grid detail page: acquisition parameters, tags, and the tilt-series list with status, rating, tags, and processing state.]]

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 ==

[[File:CryoNAV jobs.png|center|thumb|800px|Jobs page with status badges and progress.]]

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 ==

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 ==

[[File:CryoNAV admin compute.png|center|thumb|800px|Compute backend configuration (admin only).]]

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 ==

* [[CryoNAV Quick Start Guide|Quick Start Guide]]
* [[CryoNAV Grid Visualization Tools|Grid Visualization]]
* [[CryoNAV Walkthroughs|Walkthroughs]]

[[Category:Reference]]

File:CryoNAV tilt series detail.png

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Admin: Bot edit via cryonavedit.py: add pipeline and tilt-series detail screenshots

CryoNAV tilt series detail page (mock data)

File:CryoNAV pipeline.png

2026-05-20T21:56:57Z

Admin: Bot edit via cryonavedit.py: add pipeline and tilt-series detail screenshots

CryoNAV per-tilt-series pipeline view (mock data)

CryoNAV Interface Tour

2026-05-20T21:43:17Z

Admin: Bot edit via cryonavedit.py: bump cleanup thumb size to bust cache

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 ==

[[File:CryoNAV dashboard.png|center|thumb|800px|Dashboard: recent projects (top) and recent jobs (bottom).]]

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 ==

[[File:CryoNAV projects.png|center|thumb|800px|Projects list.]]

The full project list, with owner, tilt-series count, and storage. Projects are the unit of access control (see [[CryoNAV Key Concepts|Key Concepts]]). The '''New Project''' button creates an empty project that grids can then be imported into.

[[File:CryoNAV project detail.png|center|thumb|800px|A project's overview page with members, tags, and counts.]]

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 ==

[[File:CryoNAV grids.png|center|thumb|800px|Project grids tab.]]

The Grids tab lists the physical EM grids attached to the project, in the order they were imported via [[CryoNAV Tilt Series Data Collection Import|SmartScan]].

[[File:CryoNAV grid detail.png|center|thumb|800px|Grid detail page: acquisition parameters, tags, and the tilt-series list with status, rating, tags, and processing state.]]

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.

== Jobs ==

[[File:CryoNAV jobs.png|center|thumb|800px|Jobs page with status badges and progress.]]

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 ==

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 ==

[[File:CryoNAV admin compute.png|center|thumb|800px|Compute backend configuration (admin only).]]

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 ==

* [[CryoNAV Quick Start Guide|Quick Start Guide]]
* [[CryoNAV Grid Visualization Tools|Grid Visualization]]
* [[CryoNAV Walkthroughs|Walkthroughs]]

[[Category:Reference]]

CryoNAV Data Storage Backup

2026-05-20T21:43:15Z

Admin: Bot edit via cryonavedit.py: bump cleanup thumb size to bust cache

CryoNAV is designed for single-server deployment with a simple, file-based storage model: SQLite for metadata, the host filesystem for raw and processed image data.

== Database storage ==

The database stores only metadata, file paths, processing parameters, and state. It remains small (tens of megabytes even for large projects) and can be backed up with a single file copy.

The database schema mirrors the physical cryo-ET workflow: Projects contain Grids, which contain Search Maps and Tilt Series, from which Processing Runs produce Tomograms and Denoised Tomograms. Cryo-FIB images from instruments such as the Aquilos are stored as a dedicated entity linked to grids.

In addition to file paths, the database records the size of all tracked files (raw data, intermediate outputs, final results), enabling the storage monitoring described below.

== Storage monitoring ==

The '''Storage''' page in the CryoNAV interface provides an overview of disk usage across raw data, intermediate processing files, and final outputs for all projects, helping teams monitor their storage footprint and identify candidates for cleanup.

== Selective cleanup ==

[[File:CryoNAV storage cleanup.png|center|thumb|720px|Storage Cleanup tab: pick intermediate files to delete while retaining raw data and processing records.]]

Through the interface, users can selectively delete intermediate processing files (such as motion-corrected stacks, aligned series, or reconstruction volumes from superseded processing branches) while retaining the raw data and database records.

Because every processing step stores its complete parameter set in the database (see [[CryoNAV Metadata Management#Processing provenance|Processing provenance]]), the full pipeline can be re-executed from raw frames at any time, allowing researchers to reclaim storage without losing the ability to reproduce their results.

== Backup ==

The recommended backup model is a single-file copy of the SQLite database plus a filesystem-level backup of the underlying image storage. SQLite's simplicity makes the database portion straightforward; the image data follows the same backup model as any cryo-EM data store.

== See also ==

* [[CryoNAV Metadata Management|Metadata Management]]
* [[CryoNAV Data Sharing Archiving|Data Sharing & Archiving]]

[[Category:Modules]]

File:CryoNAV storage cleanup.png

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Admin: Admin uploaded a new version of File:CryoNAV storage cleanup.png

CryoNAV storage page, Cleanup tab (mock data)

CryoNAV Data Storage Backup

2026-05-20T21:31:48Z

Admin: Bot edit via cryonavedit.py: add storage tab screenshots

CryoNAV is designed for single-server deployment with a simple, file-based storage model: SQLite for metadata, the host filesystem for raw and processed image data.

== Database storage ==

The database stores only metadata, file paths, processing parameters, and state. It remains small (tens of megabytes even for large projects) and can be backed up with a single file copy.

The database schema mirrors the physical cryo-ET workflow: Projects contain Grids, which contain Search Maps and Tilt Series, from which Processing Runs produce Tomograms and Denoised Tomograms. Cryo-FIB images from instruments such as the Aquilos are stored as a dedicated entity linked to grids.

In addition to file paths, the database records the size of all tracked files (raw data, intermediate outputs, final results), enabling the storage monitoring described below.

== Storage monitoring ==

The '''Storage''' page in the CryoNAV interface provides an overview of disk usage across raw data, intermediate processing files, and final outputs for all projects, helping teams monitor their storage footprint and identify candidates for cleanup.

== Selective cleanup ==

[[File:CryoNAV storage cleanup.png|center|thumb|700px|Storage Cleanup tab: pick intermediate files to delete while retaining raw data and processing records.]]

Through the interface, users can selectively delete intermediate processing files (such as motion-corrected stacks, aligned series, or reconstruction volumes from superseded processing branches) while retaining the raw data and database records.

Because every processing step stores its complete parameter set in the database (see [[CryoNAV Metadata Management#Processing provenance|Processing provenance]]), the full pipeline can be re-executed from raw frames at any time, allowing researchers to reclaim storage without losing the ability to reproduce their results.

== Backup ==

The recommended backup model is a single-file copy of the SQLite database plus a filesystem-level backup of the underlying image storage. SQLite's simplicity makes the database portion straightforward; the image data follows the same backup model as any cryo-EM data store.

== See also ==

* [[CryoNAV Metadata Management|Metadata Management]]
* [[CryoNAV Data Sharing Archiving|Data Sharing & Archiving]]

[[Category:Modules]]

CryoNAV Interface Tour

2026-05-20T21:31:45Z

Admin: Bot edit via cryonavedit.py: add storage tab screenshots

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 ==

[[File:CryoNAV dashboard.png|center|thumb|800px|Dashboard: recent projects (top) and recent jobs (bottom).]]

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 ==

[[File:CryoNAV projects.png|center|thumb|800px|Projects list.]]

The full project list, with owner, tilt-series count, and storage. Projects are the unit of access control (see [[CryoNAV Key Concepts|Key Concepts]]). The '''New Project''' button creates an empty project that grids can then be imported into.

[[File:CryoNAV project detail.png|center|thumb|800px|A project's overview page with members, tags, and counts.]]

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 ==

[[File:CryoNAV grids.png|center|thumb|800px|Project grids tab.]]

The Grids tab lists the physical EM grids attached to the project, in the order they were imported via [[CryoNAV Tilt Series Data Collection Import|SmartScan]].

[[File:CryoNAV grid detail.png|center|thumb|800px|Grid detail page: acquisition parameters, tags, and the tilt-series list with status, rating, tags, and processing state.]]

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.

== Jobs ==

[[File:CryoNAV jobs.png|center|thumb|800px|Jobs page with status badges and progress.]]

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 ==

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|800px|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 ==

[[File:CryoNAV admin compute.png|center|thumb|800px|Compute backend configuration (admin only).]]

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 ==

* [[CryoNAV Quick Start Guide|Quick Start Guide]]
* [[CryoNAV Grid Visualization Tools|Grid Visualization]]
* [[CryoNAV Walkthroughs|Walkthroughs]]

[[Category:Reference]]

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CryoNAV storage page, Cleanup tab (mock data)

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CryoNAV storage page, Overview tab (mock data)

CryoNAV Data Sharing Archiving

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CryoNAV provides reporting and export tools designed to consolidate everything known about a dataset, from acquisition conditions through processing provenance to final quality assessment, into a portable form.

== Reports ==

The '''Create Report''' function produces a detailed report for a grid or project, listing every tilt series with:

* Acquisition parameters (voltage, pixel size, dose, tilt range, camera)
* Full processing history (pipeline steps run, parameters used, software versions, outcomes)
* Quality metrics derived from processing outputs (alignment residuals, CTF defocus values and fit quality, drift measurements)
* User-assigned quality annotations (star ratings, tags, comments)

These reports give a complete picture of a dataset's state, suitable for PI review, publication methods sections, or experimental records.

== Excel and CSV export ==

Tabular exports where each row represents a tilt series and columns capture acquisition metadata, processing parameters, computed quality metrics, and user ratings/tags.

* '''Excel''': preserves formatting, directly usable for sorting, filtering, and charting in spreadsheet software.
* '''CSV''': for compatibility with R, Python, and other analysis tools.

== ZIP bundle archive ==

Configurable packages where users select which data to include, for example:

* Raw frames plus the processing parameters needed to reconstruct from scratch
* Final tomogram volumes only
* Denoised tomograms only
* Any combination of the above

The exported bundle includes the associated metadata in a structured directory layout, making it suitable for sharing tailored result sets with collaborators or creating comprehensive archival packages that preserve the complete data lineage.

== Planned exports ==

Export into RELION .star files is planned, to facilitate handoff to sub-tomogram averaging pipelines. See [[CryoNAV About#Status and roadmap|Status and roadmap]].

[[File:CryoNAV export.png|center|thumb|700px|The Export page: build reports, tabular exports, and ZIP bundles of selected data.]]

== See also ==

* [[CryoNAV Metadata Management|Metadata Management]]
* [[CryoNAV Data Storage Backup|Data Storage & Backup]]

[[Category:Modules]]

CryoNAV Sample Experiment Management

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CryoNAV organizes cryo-ET experiments around a hierarchical data model (see [[CryoNAV Data Lifecycle|CryoEM Data Lifecycle]] for the full hierarchy). The Sample & Experiment Management area of the interface covers the day-to-day operations on these entities: creating projects, importing grids, linking FIB-SEM images, and assigning roles.

== Projects, grids, and team membership ==

Projects group related experiments. Each project contains one or more grids; each grid contains search maps and tilt series. Project owners invite team members and assign roles:

* '''System Administrator''' -- manages the deployment.
* '''Project Owner''' -- manages membership and access for one or more projects.
* '''Editor''' -- can submit jobs and edit data within assigned projects.
* '''Viewer''' -- read-only access.

Multiple owners may be assigned per project, and ownership can be transferred.

== Cryo-FIB sample preparation records ==

For workflows that involve cryo-focused ion beam milling, FIB-SEM images can be attached to the corresponding grid entity (overview images, milling progress snapshots, final lamella views). These images are linked to the lamellae as they appear in the TEM atlas and search maps, providing a single location where the full life of a grid -- from FIB preparation through tomogram -- can be reviewed.

== Rating and tagging tilt series ==

Each tilt series can be rated on a 1-to-5 star scale and assigned arbitrary text tags. CryoNAV suggests common tags (''good-ctf'', ''bad-ice'', ''thick-ice'', ''contamination'', ''promising'', ''priority'', ''exclude'') but the vocabulary is open, so each lab can develop its own conventions. Tags are color-coded for visual distinction. Combined filter expressions allow batch selection by rating and tag (e.g., "rating >= 4 AND NOT tagged 'bad-ice'").

[[File:CryoNAV tags.png|center|thumb|700px|The Tags page (admin/managers): central registry of tags with scope, usage count, and creator.]]

== See also ==

* [[CryoNAV Data Lifecycle|CryoEM Data Lifecycle]]
* [[CryoNAV Key Concepts|Key Concepts]]
* [[CryoNAV Grid Visualization Tools|Grid Visualization]]

[[Category:Modules]]

CryoNAV Interface Tour

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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 ==

[[File:CryoNAV dashboard.png|center|thumb|800px|Dashboard: recent projects (top) and recent jobs (bottom).]]

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 ==

[[File:CryoNAV projects.png|center|thumb|800px|Projects list.]]

The full project list, with owner, tilt-series count, and storage. Projects are the unit of access control (see [[CryoNAV Key Concepts|Key Concepts]]). The '''New Project''' button creates an empty project that grids can then be imported into.

[[File:CryoNAV project detail.png|center|thumb|800px|A project's overview page with members, tags, and counts.]]

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 ==

[[File:CryoNAV grids.png|center|thumb|800px|Project grids tab.]]

The Grids tab lists the physical EM grids attached to the project, in the order they were imported via [[CryoNAV Tilt Series Data Collection Import|SmartScan]].

[[File:CryoNAV grid detail.png|center|thumb|800px|Grid detail page: acquisition parameters, tags, and the tilt-series list with status, rating, tags, and processing state.]]

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.

== Jobs ==

[[File:CryoNAV jobs.png|center|thumb|800px|Jobs page with status badges and progress.]]

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 ==

[[File:CryoNAV storage.png|center|thumb|800px|Storage overview across projects.]]

The Storage page summarises disk usage per project, broken down into raw data, intermediate processing files and final outputs. From here, intermediate files from superseded processing branches can be selectively deleted while retaining the raw frames and the database record (see [[CryoNAV Data Storage Backup|Data Storage & Backup]]).

== 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 ==

[[File:CryoNAV admin compute.png|center|thumb|800px|Compute backend configuration (admin only).]]

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 ==

* [[CryoNAV Quick Start Guide|Quick Start Guide]]
* [[CryoNAV Grid Visualization Tools|Grid Visualization]]
* [[CryoNAV Walkthroughs|Walkthroughs]]

[[Category:Reference]]

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CryoNAV admin backup page (mock data)

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CryoNAV admin monitoring page (mock data)

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CryoNAV admin users page (mock data)

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CryoNAV settings page (mock data)

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CryoNAV export page (mock data)

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CryoNAV tags page (mock data)

CryoNAV Interface Tour

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CryoNAV grid detail view with tilt-series list (mock data)

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CryoNAV project grids view (mock data)

MediaWiki:Sidebar

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