Hello there in Boston. I’m new to CellProfiler and need some help. We at NMH/Feinberg are working to identify abnormal lung cells for a study looking at the possible correlation of chorioamnionitis and asthma. We want to identify, count, and measure (relative area) of the brown-stained cells on the blue background of the images. I have taken a stab at a pipeline, but really unsure of my programming and of the results. My pipeline attempt, the images (both color and black+white “bw” versions, and the output) are all attached here for you to review.
I have many questions:
Can color images be used? I tried but ran into error msgs, so converted to bw and that’s the output attached here.
How do I properly color threshold?
How to I determine pixel size of objects I want to measure - like a size threshold?
Know my efforts are very rudimentary, but we really want to put your package to use as it would greatly facilitate our work in this and other studies. Would also like to become better acquainted with Cellprofiler in general.
Many thanks in advance,
Perinatal Pathology Research Assistant
Department of Pathology, Northwestern University Feinberg School of Medicine
Clinical Research Associate
Department of Pediatrics, Division of Neonatology
Ann and Robert H. Lurie Children’s Hospital
320 E. Superior St., Searle 4-490
Chicago, Illinois 60611
DefaultOUT__2.mat (723 KB)
1stPipelineAttempt42013.cp (6.62 KB)