Contents

  • connect_zen_black

    • class ConnectMicroscope()

      • Methods for Experiment Settings

      • Methods to Save and Load Images

      • Methods to Acquire Images

      • Methods to Interact with Image Display

      • Methods to Control XY Stage

      • Methods to Control Focus

      • Methods to Interact with Objectives

      • Methods to Control Immersion Water Delivery

      • Methods to Collect Microscope Information

      • Methods to Collect Experiment Information

connect_zen_black¶

Control of Zeiss ZEN Black software. This software is used to control Zeiss spinning disk microscopes. ZEN Black uses VBA as macro language. This macro interface allows fine grained control of almost all aspects of the microscope. A subset of the classes used in the macro language are exposed as dll and are called by the class ConnectMicroscope() in module connect_zen_black.

class ConnectMicroscope()¶

Class to control Zeiss hardware through the Zeiss software Zen Black.

Methods for Experiment Settings¶

Methods to Save and Load Images¶

Methods to Acquire Images¶

Methods to Interact with Image Display¶

Methods to Control XY Stage¶

Methods to Control Focus¶

Methods to Interact with Objectives¶

Methods to Control Immersion Water Delivery¶

Methods to Collect Microscope Information¶

Methods to Collect Experiment Information¶

Microscope Automation

Navigation

Overview

  • README
  • Installation
  • Packaging the ZIP
  • Allen Institute Contribution Agreement

Orchestrator

  • find_positions
  • microscope_automation package
  • write_zen_tiles_experiment

Hardware

  • hardware_components
  • hardware_control
  • hardware_control_3i
  • hardware_control_zeiss
  • RS232
  • setup_microscope

Samples

  • correct_background
  • draw_plate
  • find_well_center
  • find_cells
  • interactive_location_picker_pyqtgraph
  • positions_list
  • samples
  • setup_samples
  • tile_images

Connectors

  • connect_slidebook
  • connect_zen_blue
  • connect_zen_black

Settings

  • meta_data_file
  • preferences
  • slidebook_experiment_info
  • zen_experiment_info

Utility

  • automation_exceptions
  • automation_messages_form_layout
  • error_handling
  • get_path
  • image_AICS
  • load_image_czi
  • software_state

Import Helpers

  • 3i Imports
  • Zeiss Imports

Reference Docs

  • LICENSE

Related Topics

  • Documentation overview
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