Main User Interface and Functions - LeonieZ/ACCEPT GitHub Wiki

The main user interface of the ACCEPT toolbox is visualized below. The main components are the chosen processing task, input and output folder, the sample list and the "Process" and "Visualize" buttons. For more information about choosing the right processor and specifying the folder see the page on Loading and Processing of Samples.

In the sample list all samples found in the specified input folder are listed and are marked in red if they are not processed before (with respect to this sample processor and this output folder) and green if a result of that sample is already saved in your output folder. Next to it there is a little checkbox for each sample that selects that sample for further processing and/or visualization. Apart from the two main buttons ("Process" and "Visualize") there are three more:

Gate: If you click on the "Gate" button, you first have to select if you want to specify a new gate or load an existing gate (more details can be found on the Design of Linear Gates page). If you selected samples by ticking the checkbox, only selected samples are gated otherwise the gate is applied to all samples and samples that are not processed before will be processed with the selected processor.

Summary: If you click on the “Summary” button, you can first select, if you want a summary of all samples in the list or only the selected ones (Figure ). You can then specify where you want to save the summary excel file. The created excel file will contain for every listed sample the number of events that fall into a certain gate and will list all gates found in one of the listed samples.

Thumbnails: If you click on the "Thumbnails" button, you have to specify if you want to export all thumbnails or only selected thumbnails that were classified before (for example by using a gate). Note that we restricted the number of saved thumbnails from a specified class to 200 images. If there are more cells that are classified in the class you selected before, 200 images are randomly picked. This should prevent that thousands of thumbnails are saved to your disk. The exported images are not optimized to be used in presentations or publications but to be processed by the thumbnail-based processors of the toolbox.