[HN Gopher] Why Recursion Pharmaceuticals abandoned cell paintin...
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       Why Recursion Pharmaceuticals abandoned cell painting for
       brightfield imaging
        
       Author : abhishaike
       Score  : 63 points
       Date   : 2024-12-12 16:08 UTC (3 days ago)
        
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 (TXT) w3m dump (www.owlposting.com)
        
       | Mistletoe wrote:
       | I find this fascinating. I used to do high content screening of
       | cells with machines like the Perkin Elmer Operetta and lots of
       | dyes. I would have never thought machine learning would make us
       | go full circle back to brightfield.
       | 
       | The meat of this article:
       | 
       | > The trend of ML in general over the past 15~ years has been to
       | strip away more and more of the biases you've encoded about your
       | dataset as you feed it into a model. Computer vision went from
       | hand-crafted interpretable features (e.g. number of circles,
       | number of black pixels when thresholded, etc), to hand-crafted
       | uninterpretable features (e.g. scale invariant feature
       | transform), to automatically extracted uninterpretable features
       | (e.g. hidden dimensions of a convolutional neural network). In
       | other words, the bitter lesson; pre-imposing structure on your
       | data is useful for a human, but detrimental to a machine.
       | 
       | The gist of it I understood is that ML could already tell and
       | label the organelles and cell structure in brightfield imaging
       | without the dyes and that adding those on top just muddled and
       | hindered it.
        
         | whatshisface wrote:
         | It makes a lot of sense in retrospect because all the
         | structures are visible on the brightfield image - it's just
         | more annoying for a human being to pick out the features on
         | thousands of slides.
         | 
         | I wonder what the dye budgets and spectral bands will go to now
         | that there is no need to mark the boundary of the nucleus. I
         | bet there are a lot of things that are not visible in the
         | refractive index that you could dye.
        
       | _ihaque wrote:
       | My team did part of the work described in TFA, AMA.
        
         | shaunregenbaum wrote:
         | Do you guys have high hopes for video data? Were there early
         | results that showed promise for kinetic data?
        
           | _ihaque wrote:
           | Yes, we (and plenty of others) have prior data showing that
           | perturbations (things that you can do to cells, like knocking
           | out genes or putting drug-candidates on them) have different
           | effects at different times, so we are excited to see the
           | potential for time course imaging.
           | 
           | Note that "video" is a little different here than the way we
           | all usually think of it - think "minutes or hours between
           | frames" not "frames per second".
        
         | _ihaque wrote:
         | I should point out that we are hiring! Software engineering,
         | data science/ML, and IT positions are available in Salt Lake
         | City, Toronto, New York, and London:
         | 
         | https://job-boards.greenhouse.io/recursionpharmaceuticals
        
           | selimthegrim wrote:
           | Do you guys have a cooldown period for applications?
        
             | ldsldslds wrote:
             | they dont respond to cold apps in my experience, except
             | canned rejection after a few months for some reason
        
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