Modernizing histopathological analysis: a fully automated workflow for the digital image analysis of the intestinal microcolony survival assay

BackgroundManual analysis of histopathological images is often not only time-consuming and painstaking but also prone to error from subjective evaluation criteria and human error. To address these issues, we created a fully automated workflow to enumerate jejunal crypts in a microcolony survival assay to quantify gastrointestinal damage from radiation. Methods and MaterialsAfter abdominal irradiation of mice, jejuna were obtained and prepared on histopathologic slides, and crypts were counted manually by trained individuals. The automated workflow (AW) involved obtaining images of jejunal slices from the irradiated mice, followed by cropping and normalizing the individual slice images for resolution and color; using deep learning-based semantic image segmentation to detect crypts on each slice; using a tailored algorithm to enumerate the crypts; and tabulating and saving the results. A graphical user interface (GUI) was developed to allow users to review and correct the automated results. ResultsCrypts counted manually exhibited a mean absolute percent deviation of (34 {+/-} 26)% between individuals vs the group mean across counters, which was reduced to (11 {+/-} 6)% across the 3 most-experienced counters. The AW processed a sample image dataset from 60 mice in a few hours and required only a few minutes of active user effort. AW counts deviated from experts mean counts by (10 {+/-} 8)%. The AW thereby allowed rapid, automated evaluation of the microcolony survival assay with accuracy comparable to that of trained experts and without subjective inter-observer variation. HighlightsO_LIWe fully automated the digital image analysis of a microcolony survival assay C_LIO_LIAnalyzing 540 images takes a few hours with only minutes of active user effort C_LIO_LIThe automated workflow (AW) is just as accurate as trained experts C_LIO_LIThe AW eliminates subjective inter-observer variation and human error C_LIO_LIHuman review possible with built-in graphical user interface C_LI Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=81 SRC="FIGDIR/small/627578v1_ufig1.gif" ALT="Figure 1"> View larger version (40K): org.highwire.dtl.DTLVardef@4d178eorg.highwire.dtl.DTLVardef@1457d39org.highwire.dtl.DTLVardef@120644eorg.highwire.dtl.DTLVardef@1996992_HPS_FORMAT_FIGEXP M_FIG C_FIG