CnrLwlss
commented
1 year ago Hi Miquel,
Great to hear from you.
This is an interesting problem. I have used colonyzer to quantify the amount of redness in colonies previously, but I'm not sure we've ever attempted to generate growth curves from red colonies. I can see how contrast could be an issue.
I haven't worked in this field for many years, so I'm not sure how much use I can be to you, but you could attempt to regularize the images somehow before analysis. Something crude you could try would be to split out the red channel only, copy that to the green and blue channels of a blank image and try to analyse that? We did some work before to quantify the degree of redness of each pixel. It could help if you created a pseudoimage where each pixel was "degree of redness".
Possibly a more promising approach would be to try to use baColonyzer, which is an updated version of Colonyzer that has been under active development much more recently: https://judithbergada.github.io/bacolonyzer/usage/
Please let me know how you get on. If I think of anything else I'll let you know. Happy to answer what questions I can, but I haven't worked on microbiology at all for the past six years or so.
All the best,
CONOR.
On Thu, 27 Apr 2023 at 14:58, MikiSchikora @.***> wrote:
Good afternoon,
Thanks for developing this tool. I am trying to analyze a 96-well plate of yeasts grown on congo red agar and I am getting misleading results. I get highly underestimated growth / cell density measurements, as compared to the growth in typical YPD plates. For instance, yeasts that appear visually to be growing well in the congo red plate may get growth measurements that are ~10% of their YPD counterparts.
The congo red plate is very red, and I suspect that the lesser contrast between the white yeasts and the red background could be the problem. Have you faced similar issues? Can you think of a simple solution to the problem? I am executing colonyzer --greenlab --lc --diffims --plots --remove --initpos --fmt 96, with version Colonyzer2==1.1.22.
Thanks,
Miquel Àngel Schikora Tamarit Barcelona Supercomputing Center
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MikiSchikora
Good afternoon,
Thanks for developing this tool. I am trying to analyze a 96-well plate of yeasts grown on congo red agar and I am getting misleading results. I get highly underestimated growth / cell density measurements, as compared to the growth in typical YPD plates. For instance, yeasts that appear visually to be growing well in the congo red plate may get growth measurements that are ~10% of their YPD counterparts.
The congo red plate is very red, and I suspect that the lesser contrast between the white yeasts and the red background could be the problem. Have you faced similar issues? Can you think of a simple solution to the problem? I am executing
colonyzer --greenlab --lc --diffims --plots --remove --initpos --fmt 96, with versionColonyzer2==1.1.22.Thanks,
Miquel Àngel Schikora Tamarit Barcelona Supercomputing Center