I am writing on behalf of my daughter. Mikaela is quite a serious young scientist (14), having won gold and platinum medals (biotechnology) at last year’s national science fair competition with her study of algal species interactions in bioreactors. She is extending her research this year with an investigation of population dynamics - more specifically the robustness and performance of multi-species cultures under non equilibrium conditions.
Mikaela is looking to use Cell Profiler to track cell populations from samples taken from continuoulsy running chemostats. The hope is that CP will be able to count AND classify up to three morphologically distinct freshwater algal species:
Scenedesmus Obliquus (SO) - oblong cells connected in four-cell coenobia
Chlorella Vulgaris (CV) - round
Pseudokirchneriella subcapitata (PS)
The unstained cells are being imaged in cell count chambers. The CP challenge is to create accurate outlines of the cells. The interior detail is not important to the study.
I have been attempting to help Mikaela set up the pipelines and we’ve had success with getting accurate counts and cell outlines for two of the three species (the round CVs and oblong SOs). However, finding a CP configuration that can consistently distinguish between all three species continues to elude.
With regards to staining: As there will be over 1,000 samples taken, a lengthy staining procedure is not really viable - unless there is some essentially instant contrast enhancement technique that can be applied during the sampling. e.g. Filters? Thoughts?
With regards to the quality of the current imagery - Our ‘home lab’s’ generic microscope has illumination and spherical aberration limitations that became very apparent once working with CP. The halo effect around the cell bodies may turn out to be our main problem. Fortunately a microscope manufacturer has offered to loan Mikaela clinical grade equipment so image quality should not be an issue in the near future.
Despite the optical challenges, I believe we’ve made pretty good progress on pipelines and we’re anxious to get some early feedback as to whether we’re on the right track.
Please find attached:
a) An image series of a mixed algal species culture (SO and PS cells), and
b) A pipeline that can be tweaked in various directions (relative weight color channel, thresholds, etc) to do a good job counting and tracing the cell boundaries of the CV and SO cells. However the PS cells do not have the same level of interior contrast. Tuning the pipeline to do a fair job on tracing PS cell boundaries causes the SO four cell coenobia to trace as two cell blobs instead of four distinct cells. The provided pipeline tuning is a compromise. The pipeline includes further comments in the module notes.
Mikaela would greatly appreciate any advice that could be offered.
Chuck b/o Mikaela