Enabling new LED illumination channels

We have finally added our three epi-illumination fluorescence LED channels to the inverted SQUID hardware and connected them to the LED connectors of the controller. We haven’t been able to identify yet where and how to configure the channels, so that the correct (or any for that matter) light is turned on. Could you please point us in the right direction?

The first five 4-pin 8 mm LED connectors from left to right are mapped to “405”, “488”, “561”, “638” and “730”. You for you can update the channel name by editing the channel_configurations.xml file (e.g. by changing Fluorescence 405 nm Ex to Fluorescence 375 nm Ex.

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Thank you! That order assignment was an important information. We did see the xml before but the reason it didn’t work before was an error in the environment installation (a mix of mamba and pip installations). Now it’s all working and I just relabelled the 561 channel to 638 in order not to have to move the driver board inside the controller.

With the environment reinstallation, now also the LED matrix variations (right, left, etc) started working. Question: How do you generate the computational phase contrast images? Do you take the images separately and compute them with a script, or is there a SQUID-specific implementation?

Here’s the code from Waller lab: GitHub - Waller-Lab/DPC_withAberrationCorrection: M. Chen, Z. F. Phillips, and L. Waller, Quantitative differential phase contrast (DPC) microscopy with computational aberration correction, Opt. Express 26(25), 32888-32899 (2018).. We’re working on some improvement and will keep you posted.

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