This is a special feature that is provided for comparing tracks obtained with the ibidi manual track tool to ACAS automatic tracking. This feature is not intended to be general purpose so it is a bit clunky.
At the bottom of this post you will find a video which demonstrates all the steps outlined here.
Create a new chemotaxis experiment and upload the well recording images as normal. This will be the automatic track.
Edit the newly created experiment and add a second well, this will be the manual track. Also, edit the names of the two wells to indicate which is manual and which is automatic (well 1 is automatic).
Be careful to upload the manual track file as metadata before uploading the well images. If the well images are upload first, automatic tracking will be begin immediately. Click the advanced checkbox in the file upload dialog and then select the 'metadata' box. Then select the manual track file to upload.
Upload the same image files previously uploaded into well-1. The manual tracks will be overlay-ed on these images.
Edit the main experiment settings and set the "Minimum Track Duration" and "Movement Threshold" settings. Then save the settings. If a report job has already been started, then click re-do on the report icon (so that these settings are used the report). Here you can find an explanation of chemotaxis settings.