Accession number BBBC002 · Version 1
Example image
Biological application
Five different samples of Drosophila melanogaster Kc167 cells were stained with Hoechst 33342, a DNA stain. The last sample (labeled nodsRNA) is of wild-type cells. Each of the other four samples (labeled 48, 340, Anillin, and mad2) has a different gene knocked down by RNAi. The sample preparation is described in more detail by Carpenter et al. (Genome Biology, 2006).
Images
There are 10 fields of view of each sample, for a total of 50 fields of view. The images were acquired on a Zeiss Axiovert 200M microscope. The images provided here are a single channel, DNA. The image size is 512 x 512 pixels. The images are provided as 8-bit TIFF files.
BBBC002_v1_images.zip (3.4 MB)
Ground truth 
A tab-delimited text file contains the number of cells in each image, as determined by two different human counters. To compare an algorithm's results to these, first compute for each sample the algorithm's mean cell count over the 10 images of the sample. Next, calculate the absolute difference between this mean and the average of the humans' counts for the sample, then divide by the latter to obtain the deviation from ground truth (in percent). The mean of these values over all 5 samples is the final result.
Note: The two human observers vary by 16% for this image set.
Published results using this image set
|
|
Citation |
|---|---|
| 17% | Carpenter et al., Genome Biology, 2006. See Figure 2A, pages 6-7. |
Nosova SA, Turlapov VE (2019) Detection of Brain Cells in Optical Microscopy Based on Textural Features with Machine Learning Methods. Program Comput Soft 45, 171–179. / doi.
Acknowledgements
We would like to thank Robert Lindquist and JooHan Chang for counting the cells.
Recommended citation
"We used the image set BBBC002v1 [Carpenter et al., Genome Biology, 2006] from the Broad Bioimage Benchmark Collection [Ljosa et al., Nature Methods, 2012]."