File Browser Guide

The File Browser is your central hub for managing all files in your workspace. This guide covers the complete left sidebar, including user information, workspace controls, file management, and navigation.

Caption: The workspace sidebar showing user info, workspace controls, file browser, and navigation

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Quick Start

1. Select a category — Choose a file type from the category dropdown (Raw Images, Annotations, etc.)
2. Upload files — Click the upload button or drag-and-drop files onto the sidebar
3. Navigate files — Click folder arrows to expand/collapse, click files to select
4. Perform actions — Right-click any file for the context menu with download, rename, and delete options
5. Use batch operations — Select multiple files with checkboxes, then download as ZIP or delete in bulk

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Detailed Guide

Sidebar Overview

The left sidebar contains the File Browser along with user information, workspace controls, and navigation. Here's the complete layout from top to bottom:

Complete sidebar layout from top to bottom

Section	Description
User Info	Your name, account status, and logout button
Workspace Info	Help icon, download button, and workspace statistics
File Browser	Upload controls, search, and file tree
Sidebar Footer	Navigation and theme controls

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User Info Section

At the top of the sidebar, you'll find your account information:

User info section displaying account details and logout option

Element	Description
User Name	Your full name as registered
Account Status	Shows your approval status (Pending, Active, etc.)
Logout Button	Click to sign out and return to the welcome page

Note: Users with "Pending" status can explore the workspace and use test data, but cannot upload custom files until approved by an administrator.

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Workspace Info Section

Below the user info, you'll find workspace controls and statistics:

Workspace info section with help icon, download button, and storage statistics

Element	Description
Help Icon	Opens the Help & Info panel with documentation and glossary
Download Workspace	Downloads your entire workspace as a ZIP archive
Files	Total number of files in your workspace
Size	Total size of all files in your workspace

Download Workspace Button

Click this button to export your entire workspace:

• Creates a ZIP archive named workspace_<timestamp>.zip with all your files
• Includes uploads, results, and models with folder structure preserved
• Excludes cache directories (.thumbnails, .slices, .mesh-previews, .preprocess, .segcleanup) — all regenerated automatically after a restore
• Useful for backup or transferring to another session

Tip: Export your workspace before major experiments to create a restore point.

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File Browser Section

The main file management area with upload controls, search, and file tree:

File Browser interface with header, category dropdown, upload button, and file tree

UI Area	Description
Header	Contains the refresh button and "Select All" checkbox
Category Dropdown	Select the type of file you want to upload
Upload Button	Triggers file upload (enabled after selecting category)
Search Bar	Filter files by name, type, or category
File Tree	Hierarchical view of all workspace folders and files
Batch Toolbar	Appears when files are selected; provides bulk operations

Uploading Files

Files must be uploaded with a category designation. The category determines where files are stored and how they can be used.

Step 1: Select a Category

Click the category dropdown and choose from:

Category	Accepted Files	Purpose
Raw Images	.tif, .tiff, .mrc	Source stacks for denoising, annotation, segmentation, or inference
Annotations	.tif, .tiff, .mrc	Segmentation masks/labels for training
Model Files	.pth, .json	Pre-trained model weights and config
Restore Workspace	.zip	Restore a previously exported workspace

Note: There is no separate inference category — images you want to run inference on are uploaded as Raw Images. MRC volumes are accepted wherever TIFFs are and can be worked with the same way.

Step 2: Upload Files

Option A: Click Upload

1. Click the upload button (enabled after selecting category)
2. Select one or more files from the file dialog
3. Watch the progress bar as files upload

Option B: Drag and Drop

1. Select a category first (required)
2. Drag files from your computer onto the sidebar
3. The drop zone highlights when files are over it
4. Release to begin upload

Drag and drop upload with the drop zone highlighted

Upload Progress

During upload, you'll see:

• A progress bar filling as each file uploads
• Text showing: "Uploading X of Y: filename"
• A success notification when complete

Note: Maximum file size is 200MB per file. Account approval is required to upload custom files—pending users can only use test data.

Restore Workspace from ZIP

Replace your current workspace with a previously exported one.

1. Select "Restore Workspace" from the category dropdown
2. Select the ZIP file to upload
3. Read the warning: This will delete all current files
4. Click "Replace Workspace" to confirm
5. Wait for extraction and restoration to complete

Restore workspace confirmation dialog warning about file replacement

Warning: Restore completely replaces your workspace. All existing files will be deleted. Export your current workspace first if needed.

Navigating the File Tree

Files are organized in a hierarchical folder structure:

uploads/
  ├── raw/              → Raw image stacks (TIFF/MRC)
  ├── annotations/      → Training masks
  └── imported_models/  → External models you upload
models/
  ├── segmentation/     → Trained segmentation models (per job)
  └── denoising/        → Trained denoising models (per job)
results/
  ├── segmentation/     → Segmentation outputs
  ├── denoising/        → Denoising outputs
  ├── meshes/           → Generated 3D meshes
  ├── preprocess/       → Preprocessing outputs
  ├── stitching/        → Stitching outputs
  └── segcleanup/       → Segmentation cleanup outputs

Per-job subfolders are created on demand as modules run, so you only see the ones that hold files.

Expanding and Collapsing Folders

• Click the arrow (▶) next to a folder to expand it
• Click again (▼) to collapse
• Folders are sorted before files, alphabetically within each category

Selecting Files

• Single file: Click the checkbox next to any file
• Multiple files: Click checkboxes on multiple files
• Select all: Click the "Select All" checkbox in the header
• Clear selection: Click the ✕ button in the batch toolbar

File tree with multiple files selected using checkboxes

File Information Display

Each file in the tree shows:

Element	Description
Checkbox	For selecting the file
Thumbnail/Icon	Preview image for TIFF files, or type icon
Filename	Full name with extension
Size	Formatted file size (KB, MB, GB)
Date	Relative time ("5 minutes ago", "2 days ago")
Category Tags	Badges showing file type (training, inference, etc.)
NEW Badge	Appears briefly on newly uploaded files

Thumbnail Previews

TIFF, PNG, and JPG files display thumbnail previews instead of icons. Thumbnails are generated on-demand and cached for performance.

Single File Operations

Right-click any file to open the context menu:

Context menu with download, rename, delete, and view info options

Download

• How: Right-click → Download, or click the ⬇️ button
• Result: File downloads to your browser's default download location

Rename

• How: Right-click → Rename
• Dialog: Enter the new display name
• Behavior: Renaming changes the friendly name shown throughout the workspace only — the underlying file and its path are never touched, so lineage, downloads, and module references keep working

Tip: Use descriptive names that include the processing step or date for easier organization. Module outputs get readable, lineage-based display names automatically.

Delete

• How: Right-click → Delete
• Confirmation: A dialog asks "Delete 'filename'? This action cannot be undone."
• Result: File is permanently removed

View File Info

• How: Right-click → View Info
• Modal displays:
  • Filename and full path
  • File size, category, and tags
  • Upload timestamp
  • Voxel size (TIFF stacks): read automatically on upload and inherited by derived outputs; click the edit (✏️) button to set x/y/z spacing and unit (µm, nm, mm)
  • File ID (for technical reference)
  • Processing History: the lineage chain (Original Upload, Denoising, Segmentation, Mesh Generation, Preprocessing, Stitching, Segmentation Cleanup, Format Conversion, Duplicated, Split)

File info modal displaying metadata and processing history

View JSON

• How: Right-click a .json file → View JSON
• Result: a syntax-highlighted, read-only viewer (files over 10 MB cannot be viewed)

Convert to…

• How: Right-click → Convert to…
• Conversions: TIFF ↔ MRC (voxel size carried through), and mesh .obj to STL, PLY, or glTF (GLB)
• Result: a new file tagged converted is added to the workspace

TIFF Stack Operations

TIFF stacks have additional operations available in the context menu:

Duplicate Stack

Creates an exact copy of the TIFF stack.

• How: Right-click → Duplicate Stack
• Result: New file created as originalname_copy.tif
• Use case: Create a backup before processing, or create variants

Split Stack

Divides a multi-slice TIFF into two separate files.

• How: Right-click → Split Stack... (only available for stacks with >1 slice)
• Dialog:
  • Enter the split point (slice number)
  • Preview shows resulting slice ranges
  • Option to delete original after split
• Result: Creates originalname_part1.tif and originalname_part2.tif

Split stack dialog with slice range selector and preview

Tip: Use Split Stack to separate a Z-stack into regions of interest, or to create smaller test datasets.

Batch Operations

When one or more files are selected, the batch toolbar appears:

Batch toolbar with download, delete, and clear selection buttons

Button	Action
Download as ZIP (⬇️)	Downloads all selected files as a single ZIP archive
Delete Selected (🗑️)	Deletes all selected files (with confirmation)
Clear Selection (✕)	Deselects all files

Batch Download

1. Select the files you want to download
2. Click the download button in the batch toolbar
3. Wait for "Preparing download..." to complete
4. ZIP file downloads as workspace_files.zip

Batch Delete

1. Select the files you want to delete
2. Click the delete button in the batch toolbar
3. Confirm the deletion in the dialog
4. Files are permanently removed

Warning: Batch delete cannot be undone. Double-check your selection before confirming.

Search and Filtering

The search bar filters files in real-time as you type.

Search bar with real-time filtering results

Search Features

• Real-time: Results update as you type (300ms delay for performance)
• Multi-word: Separate words with spaces to search for any match (OR logic)
• Clear: Click the ✕ button to clear the search

What Search Matches

Search Type	Example	Matches
Filename	training	Any file with "training" in the name
Category	seg	Files in "segmentation_results" category
Keywords	mask	Files categorized as annotations
Type	model	Model files (.pth)

Category Keywords:

• Raw images: raw, image, input
• Annotations: annotation, mask, label
• Models: weights, model, pth; config files: config
• Segmentation: segmentation, segment, result
• Denoised: denoising, denoised, clean
• Meshes: mesh, 3d, surface
• Module outputs: preprocess, stitching, segcleanup; recipes: recipe; reports: report, csv
• Test data: test

Search Results View

When searching, the file tree switches to a flat list view showing:

• File icon/thumbnail
• Filename
• Directory path (📁 path/to/file)
• Result count

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Sidebar Footer

At the bottom of the sidebar are navigation and display controls:

Sidebar footer with navigation and theme toggle controls

Element	Description
Back to Hub	Returns to the workspace hub (module selection screen)
Theme Toggle	Switches between light and dark display modes

Back to Hub Button

Click "Back to Hub" to:

• Exit the current module
• Return to the workspace hub
• View all available modules
• Access a different processing workflow

Theme Toggle

Switch between light and dark modes:

• Light Mode: Bright background, ideal for well-lit environments
• Dark Mode: Dark background, reduces eye strain in low light
• Your preference is saved and persists across sessions

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Keyboard Shortcuts

Shortcut	Action
ESC	Close open dialogs (file info, split dialog, context menu)
Tab	Navigate between interactive elements
Enter	Confirm dialogs

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Troubleshooting

Issue	Cause	Solution
Upload button disabled	No category selected	Select a category from the dropdown first
"Account approval required" error	Pending user status	Wait for admin approval or use test data
File not appearing after upload	Display not refreshed	Click the refresh button (🔄)
Rename doesn't change the downloaded filename	Rename is display-name-only	Expected — the underlying file keeps its path; the display name is what the workspace shows
Drag-and-drop not working	No category selected	Select a category before dragging files
Split Stack not available	Single-slice TIFF	Option only appears for multi-slice stacks
Search not finding file	Spelling or category	Try different keywords or clear search

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Related Help Articles

• Getting Started — Overview of the workspace
• Quick Annotation Tool — Creating annotation files for training
• Raw Training Images — Requirements for training image data
• File Upload — Uploading files to the workspace
• File Categories — Understanding file organization