Welcome to TissueMAPS’s documentation!

Contents:

• Introduction
  • What is TissueMAPS?
  • Client-server architecture
    • Client code
    • Server code
  • Browser-based user interface
    • Viewer
    • Workflow Manager
  • RESTful active programming interface
  • Distributed image processing
    • Canonical workflow
  • Interactive analysis tools
• Installation
  • Clients
    • TmClient
  • Server
    • Public cloud images
    • Docker
    • TmDeploy
• User guide
  • Interacting with the server
    • User interface
    • RESTful programming
  • Using the library
    • Application programming interface (API)
    • Command line interface (CLI)
• Developer guide
  • Frontend
    • Architecture
    • Data access objects (DAO)
    • Dialogs
    • Viewer
    • Data analysis tools
    • HTTP client interfaces
  • Backend
    • Documentation
    • Coding style
    • Tests
    • Server development
    • Library development
    • Jterator module development
• Support and troubleshooting
  • Issue tracker
    • Creating an issue
  • Debugging
    • Using dev servers
• License
  • Client code
  • Server code
• Packages
  • tmlib package
    • Module contents
    • Subpackages
    • Submodules
    • tmlib.config module
    • tmlib.errors module
    • tmlib.formats module
    • tmlib.image module
    • tmlib.import_utils module
    • tmlib.jobs module
    • tmlib.log module
    • tmlib.metadata module
    • tmlib.readers module
    • tmlib.submission module
    • tmlib.utils module
    • tmlib.version module
    • tmlib.writers module
  • tmserver package
    • Module contents
    • Subpackages
    • Submodules
    • tmserver.appfactory module
    • tmserver.config module
    • tmserver.error module
    • tmserver.serialize module
    • tmserver.util module
    • tmserver.version module
  • tmclient package
    • Submodules
    • tmclient.base module
    • tmclient.api module
    • tmclient.log module
    • tmclient.version module
    • Module contents
  • tmdeploy package
    • Submodules
    • tmdeploy.config module
    • tmdeploy.errors module
    • tmdeploy.inventory module
    • tmdeploy.log module
    • tmdeploy.utils module
    • tmdeploy.version module
    • Module contents
  • jtlib package
    • Module contents
    • Submodules
    • jtlib.features module
    • jtlib.plotting module
    • jtlib.utils module
    • clip module
    • combine_channels module
    • combine_masks module
    • expand module
    • fill module
    • filter module
    • invert module
    • label module
    • measure_texture module
    • measure_intensity module
    • measure_morphology module
    • register_objects module
    • relabel module
    • segment_secondary module
    • separate_clumps module
    • smooth module
    • threshold_adaptive module
    • threshold_manual module
    • threshold_otsu module
• Frequently Asked Questions (FAQ)
  • Why don’t you use HDF5 as a container for all data?
  • Does TissueMAPS run on GPUs?

Indices and tables

• Index
• Module Index
• Search Page