4. Filter and Finalize

Cell detection workflow — Step 4

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

  1. Review and/or edit the cell-detection settings carried over from step 3. Preview.

    Detection setup

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

      Note that the channel is automatically set to Adj. image if, in the previous step, you selected Image adjustment result under Image Source.

    • 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.

  2. Fine tune the filter strength

    Strength Filter: Follow the instructions in the workflow window:

    1. Click Detect to detect cells according to the settings you have selected.

    2. Adjust the filter strength by re-positioning the black and red lines in the histogram to mark the start and end of the cell-signal strength values you want to use for automatic cell detection.

  3. Choose the marker for your detected cells.

    Select the marker to use for detected cells from the drop-down menu.

    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 BrainMaker window.

    • Choose Customize in File > Preferences > Tracing > Markers

  4. Finish the workflow.

    To generate markers for the detected cells, click the Finalize button.

  5. (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

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

Commands present in all steps of the 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.

 New workflow: Click the new workflow button to start over; the settings will revert to those specified in the previous completed workflow.

 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.