[BioCam]

The Problem

A filter in the CLARIOstar's slides can only be used by building its OpticalFilter or DichroicFilter by hand, with band edges the user has to know - although the reader can scan its own filters. And there is no way to find the focal height of a sample: every read takes either the default (25 % of the well depth) or a height given explicitly, both guessed, while the signal can fall to half a few millimetres from its peak.

PR Content

• Fluorescence.detect_all_filters() scans the reader's 11 filter positions and returns its three slides: excitation, dichroic, emission. Each position holds the filter found there with its band, or nothing if it is empty. The slides are also kept as excitation_filter_slide, dichroic_filter_slide and emission_filter_slide.

  

• A FluorescenceChannel filter can then be given by its position on its slide (excitation_filter=1), or by the name of a filter assigned to the slide.

• Fluorescence.measure_z_profile(fluorescence_channel, well=...) runs the reader's z-scan of one well, in 0.1 mm steps down from maximum_focal_height. The CLARIOstarZProfileResult holds the profile, the peak's counts and their percent of the detector's range, the timestamps, and peak_focal_height to pass to measure. With gain_target_percent the firmware also fits the gain at the peak.

• measure and measure_spectrum point to measure_z_profile for the focal height with the most signal.

• Cancelling a filter scan or a z-scan drains the reply in flight before STOP.

fluorescence = reader.fluorescence

# 1. detect the filters in the three slides, once per fitted set (about 4 minutes)
excitation_slide, dichroic_slide, emission_slide = await fluorescence.detect_all_filters()
excitation_slide[1]  # the filter at position 1 of the excitation slide, with its band

# 2. use them by their position: here position 1 of each slide
channel = FluorescenceChannel(excitation_filter=1, dichroic_filter=1, emission_filter=1)

# 3. find the focal height with the most signal, the gain fitted to 90 % of the detector's range
profile = await fluorescence.measure_z_profile(
    channel, well=plate.get_well("A1"), gain_target_percent=90
)

# 4. read the plate there
result = await fluorescence.measure(
    channel, gain=profile.gain, focal_height=profile.peak_focal_height
)

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