I guess you are referring to the video on this page: https://publiclab.org/wiki/spectral-workbench-usage, which is this video: https://www.youtube.com/watch?v=idg10MiceEI.
I have not used that feature of Spectral Workbench, and I don't know how it has changed since the video was made. Maybe someone more familiar with that feature can help.
When doing absorption spectrometry, the idea is to capture a spectrum of a light source and then put a translucent sample between the light and the spectrometer and capture another spectrum. Less light of certain wavelengths will be transmitted through the sample. When the second spectrum is captured, the exposure settings on the camera in the spectrometer cannot change. If an automatic exposure feature of the camera allows the camera to adjust to the lower light levels with the sample in place, the difference between the two spectra will not be a reliable measure of how much light the sample absorbed. Maybe someone familiar with the Public Lab spectrometer can explain how that problem is dealt with.