PUBLICATION
On the objectivity, reliability, and validity of deep learning enabled bioimage analyses
- Authors
- Segebarth, D., Griebel, M., Stein, N., R von Collenberg, C., Martin, C., Fiedler, D., Comeras, L.B., Sah, A., Schoeffler, V., Lüffe, T., Dürr, A., Gupta, R., Sasi, M., Lillesaar, C., Lange, M.D., Tasan, R.O., Singewald, N., Pape, H.C., Flath, C.M., Blum, R.
- ID
- ZDB-PUB-201021-1
- Date
- 2020
- Source
- eLIFE 9: (Journal)
- Registered Authors
- Keywords
- computational biology, mouse, neuroscience, systems biology, zebrafish
- MeSH Terms
-
- Animals
- Deep Learning
- Fear
- Fluorescent Dyes
- Image Processing, Computer-Assisted/methods*
- Male
- Mice
- Reproducibility of Results
- Signal-To-Noise Ratio
- Zebrafish
- PubMed
- 33074102 Full text @ Elife
Citation
Segebarth, D., Griebel, M., Stein, N., R von Collenberg, C., Martin, C., Fiedler, D., Comeras, L.B., Sah, A., Schoeffler, V., Lüffe, T., Dürr, A., Gupta, R., Sasi, M., Lillesaar, C., Lange, M.D., Tasan, R.O., Singewald, N., Pape, H.C., Flath, C.M., Blum, R. (2020) On the objectivity, reliability, and validity of deep learning enabled bioimage analyses. eLIFE. 9:.
Abstract
Bioimage analysis of fluorescent labels is widely used in the life sciences. Recent advances in deep learning (DL) allow automating time-consuming manual image analysis processes based on annotated training data. However, manual annotation of fluorescent features with a low signal-to-noise ratio is somewhat subjective. Training DL models on subjective annotations may be instable or yield biased models. In turn, these models may be unable to reliably detect biological effects. An analysis pipeline integrating data annotation, ground truth estimation, and model training can mitigate this risk. To evaluate this integrated process, we compared different DL-based analysis approaches. With data from two model organisms (mice, zebrafish) and five laboratories, we show that ground truth estimation from multiple human annotators helps to establish objectivity in fluorescent feature annotations. Furthermore, ensembles of multiple models trained on the estimated ground truth establish reliability and validity. Our research provides guidelines for reproducible DL-based bioimage analyses.
Genes / Markers
Expression
Phenotype
Mutations / Transgenics
Human Disease / Model
Sequence Targeting Reagents
Fish
Orthology
Engineered Foreign Genes
Mapping