NimOS Tabs

NimOS Tabs

NimOS Tabs:
Files:
  1. Load Data: open an acquisition, which will then appear in the Analyze interface.
Instrument:
  1. Instrument Config: show general information about the microscope.
  2. Manual Connect: manually select an instrument file to connect to the microscope.
  3. Calibrate Camera: calibrate the camera to remove hot/dead pixels. For detailed instructions, check here.
  4. Channel Mapping Calibration: calibrate the microscope to remove channel misalignment. For detailed instructions, check here.
  5. 3D Mapping Calibration: calibrate the microscope for 3D super-resolution imaging.
  6. Show Focus Camera View: show the focus camera.
  7. Focus Camera Settings: change the settings of the focus camera. Do not change the focus camera settings.
  8. Show Instrument Info: show additional information about the microscope.
Data:
  1. View Acquisition Data: show the metadata of the opened file.
  2. Export Localization Rendering: export super-resolution localization images. By increasing the pixel size, you are increasing the size of the export image and thus the display resolution. You can also change the point rendering, color or greyscale, and contrast. For detailed instructions, check here.
  3. Export Mapped Channels Crops To Tiff: save the mapped channels as a multipage tiff file for external processing (e.g. ImageJ). For detailed instructions, check here.
  4. Batch Processing: select to batch-export multiple sets of data from a folder. You can put all your acquisition data in one folder and choose to export them as CSV and/or mapped channels respectively. For detailed instructions, check here.
Settings:
  1. User Settings: change user-specific settings for microscope control and data I/O. For detailed instructions, check here.
  2. System Settings: set the acquisition root directory.
Advanced:
  1. Python Console: open the NimOS Python console (PythONI). For detailed instructions, check here.
  2. Log Viewer: show info/errors of the software in real-time.
Help:
  1. About: show information about the versions of NimOS and its dependencies.
  2. User Guides: show user manuals about the analysis tools.
  3. Change Logs: show information about what has been changed in the latest version of NimOS.
  4. Send Feedback: submit feedback to ONI
  5. Report Bug: link to the service desk ticket center.


    • Related Articles

    • NimOS Overview

      NimOS is the software used to control the microscope. Basic controls and terms are highlighted below. For video instructions on how to use NimOS to take an acquisition, check here. For NimOS tabs, check here. For laser control, check here. For stage ...

    • NimOS Installation Guide

      NimOS Auto-Update In theory, NimOS will pop up a window upon shutdown whenever an update is available: It is recommended to perform the update. Click on Download and Install Update to proceed with the update. The installation process will be ...

    • Temperature Control

      Temperature Control: Target: set the target temperature. All the thermistor readings can be monitored in the Microscope Box Temperature tab: Current: show the temperature feedback in real-time, averaged from all thermistors. Hover around the current ...

    • Keyboard Control

      NimOS offers several keyboard controls. To activate the keyboard control, left-click on any of the channels. Arrows: controls X/Y translation. PgUp/PgDn: controls Z translation. Ctrl: activate coarse translation (faster speed). The speed can be ...

    • Laser Control

      Light Control: A and B: allow to have 2 global laser configurations. For example, put lower power in A for preview and put higher power in B for imaging. Laser Tab: turn on/off the laser. The laser is on when the tab is light and is off when the tab ...