Workspace Guides

Step-by-step guides and best practices to help you get the most out of the BioMed Workspace.

Available Guides

Getting Started

Create your account, navigate the interface, and run your first analysis

Preprocessing Module

Crop, trim, downscale, and adjust intensity before running the pipeline

Segmentation Module

Train U-Net models for biomedical image segmentation or use pretrained models

Segmentation Cleanup Module

Paint corrections, run automated cleanup, and quantify segmentations per class

Stack Stitching Module

Join stacks in z or as mosaics, with reusable stitch recipes for sibling volumes

Deep Learning Denoising

Remove noise with auto-routed autoStructN2V and N2V self-supervised learning

Filter Denoising Module

Apply Gaussian and Non-Local Means filtering for quick noise reduction

Annotation Module

Paint ground-truth segmentation masks with brush tools and class management

Image Viewer Module

Browse TIFF stacks with gallery and thumbnail modes, zoom and pan controls

Mesh Generation Module

Convert segmentations to 3D surface meshes for visualization or 3D printing

3D Visualization Module

Explore meshes interactively with per-class visibility and opacity controls

File Browser

Upload, organize, download, and manage your workspace files

Help & Info Panel

Access contextual help articles and navigate documentation from anywhere

Best Practices

Data preparation, training tips, and resource management for optimal results

Prerequisites

Before starting these guides, make sure you:

1. Have access to the BioMed Workspace
2. Have some TIFF image stacks ready (or use the built-in test data)

Module Documentation

For detailed information about specific features, see the module documentation in the sidebar.