Cell detection workflow >

4. Filter and Finalize

Purpose

In this step, cell count and signal strength are displayed on a histogram so that you can finalize your filter settings. You can also set the marker that will be used to indicate detected cells in this step.

Procedure

Before you start

Review and/or edit the cell-detection settings carried over from step 3. Preview in the Detection setup section at the top of the window.

Detection setup

  • Channel: The color channel used for cell detection should correspond with how the specimen is labeled.

    The channel is set to Adj. image if you selected Image adjustment result in step 3 of the workflow.

  • Preset: Displays the selected preset.
  • Marker/preview: Color of the markers used for detected-cell previews and final cell-detection results.
  • Show preview results checkbox: Check or clear the box to view or hide the results of running the cell detection preview.

Procedure for detecting cells, adjusting filtering, and finalizing cell detection

  1. Click Detect to detect cells in the image plane/volume defined in Step 1 according to the settings you have selected.

    Strength Filter: Follow the remaining instructions in the workflow window:

  2. Fine tune the filter strength and choose the marker for your detected cells as follows:

    1. Drag the red and blue lines in the histogram to mark the start and end of the cell-strength values you want to include for automatic cell detection. Objects with cell strengths between the lines will be considered cells, and objects with cell strength that falls outside of the red and blue lines are excluded from cell detection results.

      Note that values for the filter strength and the number of cells that will be detected are displayed below the graph.

    2. Select the marker to use for detected cells from the drop-down menu near the bottom of the workflow window.

      You can customize the markers if desired:

      • Right-click the marker you want to change in the marker menu that runs down the left side of the NeuroInfo window.

      • Choose Customize in File > Preferences > Tracing > Markers

  3. Click the Finalize button to generate markers for the detected cells and finish the workflow.

    You will see the number of cells detected in the marker toolbar, next to the marker type you selected in step 3 above.

  4. (optional) Save the detection parameters as a preset.

    1. Click the Presets button and select Edit Presets.

    2. In the Save/Update window, type a name for the preset, then click Save

    3. Close the workflow by clicking the X in the upper right of the window.

Commands present in all steps of the workflow

New workflow: Click the new workflow button to start over; the settings will revert to the defaults or those specified in the previous completed workflow.
Previous step / Next Step: Click to advance in the workflow or revisit a previous step. Alternatively, you can click the steps listed at the top of the workflow to jump to that step.

Presets: Click to select a preset and apply those saved settings to the current workflow. Note that you can save your settings as a preset at the end of the workflow.

  • Loading an existing preset: Click Presets and select a preset from the list.

  • Saving or deleting presets: Click Presets and select Edit Presets; the Save/Update dialog box opens. You can:

    • Type a name for the preset, and click Save.
    • Select an existing preset and click Delete to remove it.