User guide - QBI-Software/AutoAnalysis_SynapticVesicles GitHub Wiki

The application consists of several panels for running the automated analysis with minimal user interaction required.

Welcome

Welcome panel

Configure

Config panel

A range of configuration options are available. These are described in the panel but to highlight a few important ones:

  1. BLEACH_FILENAME: This is the exact name of the Bleach file to be found in the same directory as the datafile
  2. DATA_FILENAME: This is a suffix to the data file name which is used when searching directories in the File Panel
  3. SELECTED_ROIS: This is the suffix of the file name containing a list of the ROIs in the data to be included in the second processing. This file needs to be manually created after the first process has run by opening the ROI list file in the 'processed' directory and deleting unwanted ROIs then saving it with this filename ending.

A configuration set can be saved by typing a new name in the dropdown and then clicking on Save Changes. To reload it, just select it from the dropdown.

Select Files

Files panel

Select a top level directory containing the required data files, provide a Filename search text if only certain types of files are required (this will search both file path and filenames and can serve as a prefix for the data unless the box is cleared before running the processes), then click AutoFind. In addition, there is the Drag'n'Drop function for individual files. The files are matched to the 'Data Filename' suffix set in the configuration panel.

Only data files need to be checked in the file list to be included in the analysis (accompanying Bleach files will be found in the same folders). A note on the data file, it should contain:

  1. Time
  2. Frame (with stimulus marked as 'STIM_X' in this column)
  3. ROI (multiple)

The output directory is required for the compiled data whereas individually processed files will be put in a subfolder ("processed") in the input directory structure.

There is also an option to group files as set by fields "Group1, Group2" in the configuration. To mark a file, first check the file, then select the group from the dropdown and click Assign. If the group names are in the paths, they will be set automatically but this can be changed as mentioned. The final file list can be saved for reloading at a later date.

Run Processes

Process panel

In this application, the processes must be run separately due to dependencies on a manual selection.

  1. Select the Bleach Averaging process first. A number of interactive plots will pop up in your browser. When it has finished, open the subfolder containing the files, find the file specified as the ROI_FILE in the Configuration panel (_ROIlist.csv) and edit it to select required ROIs, then save it as SELECTED_ROIS (_ROIlist_selected.csv).

  2. Select the Normalize Baseline process. This requires the SELECTED_ROIS to be present in the "processed" directory. An interactive plot should pop up as a scatter plot of data, with mean +/- SEM and fitted by exponential with decay and amplitude indicated on the plot.

Interactive plots can also be suppressed during processing by unchecking the checkbox if only the data files are required.

A log file is produced in the user's home directory which can be viewed by Show Log. Check this for any errors (scroll to the bottom).

Troubleshooting

Please check the log file for any obvious errors such as missing Bleach.csv file - it may just need renaming. Otherwise, send an email to the developer and/or log an issue here on github.