Function: Overview Scan

Function: Overview Scan

The Overview Scan function allows acquiring a mosaic containing multiple positions for identifying the imaging positions (e.g. cell positions):
  1. Scan Parameters: set the origin and number of tiles to acquire for X and Y.
  2. Set Initial Position as Current Stage Position: set the origin to the current position.
  3. Advanced:
    1. Frames Per FOV: set the number of frames to acquire per field of view.
    2. Stage Speed: set the translation mode to either Accurate or Fast.
    3. Focus Speed: set the focus mode to Accurate, Fast, or Off.
  4. Display Parameters: set the lower and upper threshold for the Percentiles contrast method.
  5. Channel 0/Channel 1: select the channel for preview and export.
  6. Run Scan/Cancel: start/stop the overview scan.
  7. Export To Tiff: export the rendered preview to a Tiff file.

Instructions

  1. Set the focus reference and enable the Z lock.
  2. Click on Overview Scan to open the overview window.
  3. In the pop-up window, set the origin and number of tiles for both axes, and click on Run Scan to start the scan.
  4. Once the scan is finished, navigate to a sample position by double-left-clicking in the rendered preview. Zooming in/out is also supported in the preview.

  5. Click on Export To Tiff to export the rendered preview (wide-field) to a Tiff file if needed.

Discussions

  1. The overview rendering will be cleared if you close the window and it is recommended to minimize and maximize the window.
  2. The scan will always start from the position specified in Initial X-Position and Initial Y-Position.
  3. Export To Tiff will only export the current channel (either 0 or 1).
  4. Row-major (X first) snake scanning is used, in which the stage always moves along the positive Y direction.

    • Related Articles

    • Function: Position List

      The Open Position List function allows saving/reading positions to/from a list, which can be combined with the Overview Scan function for multi-position imaging: Load From File/Save To File: load/save a position list from/to a JSON file. Label For ...

    • Function: Z Lock

      The Nanoimager has a Z Lock functionality which allows for long and stable acquisitions from the desired focal plane. This feature is very useful for multiple types of imaging including dSTORM, tracking, overview scan, and multi-position ...

    • Function: PythONI

      What's PythONI? NimOS comes with its own python IDE called PythONI (/pi thon ni/). The simple python IDE allows you to write your own automation python script for controlling almost every part of the Nanoimager. This instruction will cover what's ...

    • Function: Confocal

      The Confocal function allows the acquisition of high-resolution confocal images, which is useful when dSTORM is not viable: Enable/Disable Confocal: enable/disable the confocal mode. Enable Navigation Mode: allow to quickly navigate the sample with ...

    • Function: Multi-Acquisition

      This Article contains information on mulitacquisition from various versions of Nanoimager software. Most of the functionalities remained the same but new functionalities and some changes have been introduced in user interface. Changes in Multi ...