Tutorial 3: Adjusting Analysis by editing ini-files

This tutorial provides tips and hints how to quickly adjust analysis parameters for optimizing analysis.

Before going through this tutorial, make sure to follow tutorial 1 first.

Example 1: Altering the number of imaging positions to be analyzed

In your operating system (Windows explorer, MacOS finder, etc...), open the directory into which the tutorial data was copied (see Tutorial 1). Make sure that the directory 'data_directory' is empty. Identify the test_set.ini file. Make a copy of this file and name it modified_test_set.ini

Use a text editor (notepad on Windows/PC, TextEdit on MacOS) to open and edit the modified_test_set.ini file.

and change it to:

Save the ini-file. As in Tutorial 1, perform the automated analysis -- this time using the modified ini-file. In short: Choose NeuriteQuant_analysis from the ImageJ plugins Tab A message will open, which asks you to open a configuration file. Click OK, and browse to the directory, into which you unpacked the NeuriteQuant tutorial archive. Select the modified_test_set.ini file and click Select. Then, select the data_directory, followed by selecting the input directory The MophoJ plugin then runs it's analysis. Do not disturb the program flow.

After the run, the directory data_directory is filled with analysis results. Choose the file screen.html in the data_directory and open it with a web browser to review the analysis. In the web browser, click on the link '5a-norm Heatmaps' to review the results. You will see that after editing the ini-file, only one imaging position per condition was analyzed. Thus, setting the positions value in the ini file defines how many positions should be analyzed per condition.

Example 2: Altering analysis parameters

Now, go back to your text editor and apply some additional modifications to the modified_test_set.ini file:

Change back the positions to 3, then find the line:

methods1=cellbodies neurites endpoints cellcount report

and change it to:

methods1=cellbodies neurites cellcount report

then find the line:

parameters1=neurite_detection_width:4 neurite_detection_threshold:6 neurite_cleanup_threshold:20 neuronal_cellbody_detection_threshold:50

and change it to:

parameters1=neurite_detection_width:4 neurite_detection_threshold:6 neurite_cleanup_threshold:20 neuronal_cellbody_detection_threshold:200

finally find the line:

image_scale_min2=300

and change it to:

image_scale_min2=800

After saving the ini-file, perform the automated analysis again. At the end of the analysis, you receive a few warnings. These warnings appear because some measurements were removed in the text editing, which are still supposed to be shown in the web browser. Click OK for each of these warnings. Review the analysis result in the web browser. You will see that removing the 'endpoints' keyword from the methods1 list leads to skipping of the advanced analysis of neurite endpoints in channel 1. Endpoint analysis is still performed in channel 2. Altering the neuronal_cellbody_detection_threshold value in the parameters1 list leads to detection of fewer cellbodies in channel 1. Finally, raising the image_scale_min2 value to 800 leads to suboptimal image scaling in channel 2 and many weaker neurite structures are not detected in that channel.

In conclusion, this tutorial showed how analysis can be manipulated by editing the ini-file and how certain settings affect the analysis process. Please consult the documentation for additional information about the settings in the ini-file.