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Thread: digital microscope/ cell counting software

  1. #1
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    digital microscope/ cell counting software

    Does anyone have recommendations or advice on digital microscopes?

    I want to do basic cell counts with a haemocytometer for yeast pitching to start, and may do basic staining for viability. More advanced micro may follow in future.

    I have seen the Celestron 44341 microscope for $157 which looks like a basic entry level scope.

    I was also interested in cell counting software. internet search came up with Cell profiler and Image J as open source/ free options.

    What do other people use/ like?

  2. #2
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    I have a good amount of experience with ImageJ from my university lab, and in my opinion it just wouldn't be worth the training and fuss when cell counts through your regular microscope are very simple and useful. We have a cellometer that's collecting dust at our lab here because everything is done the ol' fashion way.

    Just my opinion of course. If you we're doing more advanced cell counting for studies and whatnot, it may be the more efficient and worth your time, but I guess it really depends on the application. Basic yeast pitching cell counts and viability, as well as wet mounts for bacteria analysis later on if you do micro are easily done without software.

  3. #3
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    Quote Originally Posted by jtidei19 View Post
    I have a good amount of experience with ImageJ from my university lab, and in my opinion it just wouldn't be worth the training and fuss when cell counts through your regular microscope are very simple and useful. We have a cellometer that's collecting dust at our lab here because everything is done the ol' fashion way.

    Just my opinion of course. If you we're doing more advanced cell counting for studies and whatnot, it may be the more efficient and worth your time, but I guess it really depends on the application. Basic yeast pitching cell counts and viability, as well as wet mounts for bacteria analysis later on if you do micro are easily done without software.
    +1

    A moxiflow or other cellometer can be a nice tool to have, but it doesn’t replace the benefits of the manual methods.

    It can be very nice to have a usb output on your Microscope though. Then you can save still shots on the computer and count or mark them as needed. You can also save and reference physical properties down the road. I’m all about embracing technology, but I don’t like things that are needlessly complicated.

  4. #4
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    thanks for the feedback.

    When i worked in a brewery lab years ago, i spent time everyday peering into a microscope doing counts. my eyes did not like it then and i am older now.

    I think that just being able to view on a larger screen will be a great improvement. i had somehow hoped that a magic counting machine could automatically count for me. I would still have to do the sample preparation. It sounds like it may be possible but the setup and tweaking of the computer will be as much work as the counting would have been.

  5. #5
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    Quote Originally Posted by beerme View Post
    [...] i had somehow hoped that a magic counting machine could automatically count for me. I would still have to do the sample preparation. It sounds like it may be possible but the setup and tweaking of the computer will be as much work as the counting would have been.
    This came up today on Reddit:

    https://www.oculyze.de/en/

    Supposedly Oculyze has already built your automagic counting machine.

    Details are in that Reddit post, but they sell a basic package (which I believe comes with both the smartphone, and the microscope, along with a basic set of supplies), and the analyses are either fixed-price or an unlimited monthly rate. I have no idea how well it works, but it's a very interesting idea.

    Regards,
    Mike

  6. #6
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    Quote Originally Posted by rdcpro View Post
    This came up today on Reddit:

    https://www.oculyze.de/en/

    Supposedly Oculyze has already built your automagic counting machine.

    Details are in that Reddit post, but they sell a basic package (which I believe comes with both the smartphone, and the microscope, along with a basic set of supplies), and the analyses are either fixed-price or an unlimited monthly rate. I have no idea how well it works, but it's a very interesting idea.

    Regards,
    Mike
    I got to see Oculyze first hand at CBC and it was very impressive. I plan on going this route for sure.
    Hop It And Bitterness Will Come

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    Half Moon Bay Brewing Co.
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  7. #7
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    Quote Originally Posted by rdcpro View Post
    This came up today on Reddit:

    https://www.oculyze.de/en/

    Supposedly Oculyze has already built your automagic counting machine.

    Details are in that Reddit post, but they sell a basic package (which I believe comes with both the smartphone, and the microscope, along with a basic set of supplies), and the analyses are either fixed-price or an unlimited monthly rate. I have no idea how well it works, but it's a very interesting idea.

    Regards,
    Mike

    Aww that takes the fun out of it!

    This is pretty neat though, automatic counting would save a ton of time when you're getting cells in suspension checks on 15 different FV's (my life). Looks like one reviewer said it was off based on data from a bunch of people's manual counts, so I'd assume they need to optimize it more before this becomes a widely used product.
    Last edited by jtidei19; 05-30-2018 at 09:46 AM.

  8. #8
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    Quote Originally Posted by jtidei19 View Post
    Looks like one reviewer said it was off based on data from a bunch of people's manual counts, so I'd assume they need to optimize it more before this becomes a widely used product.
    Exactly. I would think that if Moxiflow and Nexcelom haven't perfected it yet, that a smartphone app isn't going to cut it for lab grade accuracy. As a homebrewer/hobby it seems like a really neat idea. I talked extensively with a Nexcelom rep a few years back, and also had some inside discussions on Moxiflow before it was released. They are pretty cool tools, but they just don't have the precision of a manual count. If you are looking at bulk data processing and trending data as opposed to precision accuracy, they certainly fit the bill.

    Of course its important to remember we are looking at a drop out of billions of drops, so there are other factors at play against accuracy anyways.

    There are intricacies with the cell sizes and how they bud or clump. Most "automated bean counters" have a hard time compensating for variances. For instance, Hefe yeasts tend to link or group and may be falsely counted as one cell, or too many cells depending on the programming. Shape can effect how the cell is counted. Viability can be difficult in these strains as well. Moxiflow is even pre-loaded with White Labs strains, last I checked, to be more accurate in its counts (adjusting parameters for strain).

    I'll be interested to see how the Oculyze pans out.

  9. #9
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    Quote Originally Posted by UnFermentable View Post
    Exactly. I would think that if Moxiflow and Nexcelom haven't perfected it yet, that a smartphone app isn't going to cut it for lab grade accuracy. As a homebrewer/hobby it seems like a really neat idea. I talked extensively with a Nexcelom rep a few years back, and also had some inside discussions on Moxiflow before it was released. They are pretty cool tools, but they just don't have the precision of a manual count. If you are looking at bulk data processing and trending data as opposed to precision accuracy, they certainly fit the bill.

    Of course its important to remember we are looking at a drop out of billions of drops, so there are other factors at play against accuracy anyways.

    There are intricacies with the cell sizes and how they bud or clump. Most "automated bean counters" have a hard time compensating for variances. For instance, Hefe yeasts tend to link or group and may be falsely counted as one cell, or too many cells depending on the programming. Shape can effect how the cell is counted. Viability can be difficult in these strains as well. Moxiflow is even pre-loaded with White Labs strains, last I checked, to be more accurate in its counts (adjusting parameters for strain).

    I'll be interested to see how the Oculyze pans out.
    For sure, I'm definitely going to follow their progress.

    I can definitely see there being some difficulty for the program standardizing all strains, especially with the clumping factor and whatnot. We use sulfuric, and some strains like our house saison and weihenstephan just will not un-floc even after rigorous vortexing. I could definitely see it causing some type of counting error in this software as it's not fully optimized yet, but I'm sure the technology will get there soon!

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