CryoNAV Interface Tour - Revision history

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

2026-05-20T21:57:02Z

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

← Older revision		Revision as of 23:57, 20 May 2026
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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 ==

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

2026-05-20T21:43:17Z

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

← Older revision		Revision as of 23:43, 20 May 2026
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	'''Overview''' summarises disk usage per project, broken down into raw data, intermediate processing files, and final outputs.		'''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.]]		[[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.		'''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.

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

2026-05-20T21:31:45Z

Bot edit via cryonavedit.py: add storage tab screenshots

← Older revision		Revision as of 23:31, 20 May 2026
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	== Storage ==		== Storage ==

	~~[[File:CryoNAV storage.png\|center\|thumb\|800px\|~~Storage ~~overview across projects~~.]]		The Storage page has two tabs.

	~~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]]).		[[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 ==		== Export ==

Admin: Bot edit via cryonavedit.py: add interface screenshots

2026-05-20T21:27:38Z

Bot edit via cryonavedit.py: add interface screenshots

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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.
 == Storage ==
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 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]]).
 == 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.
 == See also ==

Admin: Bot edit via cryonavedit.py: add grid detail screenshot to Interface Tour

2026-05-20T21:12:06Z

Bot edit via cryonavedit.py: add grid detail screenshot to Interface Tour

← Older revision		Revision as of 23:12, 20 May 2026
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	[[File:CryoNAV grids.png\|center\|thumb\|800px\|Project grids tab.]]		[[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]]. ~~Each~~ grid opens a ~~card view~~ of ~~its~~ tilt series, ~~with thumbnails~~ and ~~acquisition metadata~~; see [[CryoNAV Grid Visualization Tools\|Grid Visualization]] for atlas, search-map overlay, card view and list view.		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 ==		== Jobs ==

Admin: Bot edit via cryonavedit.py: add reference pages and screenshots

2026-05-20T20:57:41Z

Bot edit via cryonavedit.py: add reference pages and screenshots

New page

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]]. Each grid opens a card view of its tilt series, with thumbnails and acquisition metadata; 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.

== 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]]).

== 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.

== See also ==

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

[[Category:Reference]]