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Liver Age
Contributors: Tomasz Macura, Suresh Poosala

The Atlas of Gene Expression in Mouse Aging Project (AGEMAP) is a study by the National Institute on Aging, National Institutes of Health, involving 48 male & female mice, of four ages (1, 6, 16, and 24 months), on ad-libitum or caloric restriction diets. Liver organs were extracted from sacrificed mice, sectioned, stained with hematoxylin and eosin (H&E), and imaged by a bright-field microscope.

Fifty color images per liver were manually acquired using a Carl Zeiss Axiovert 200 microscope and 40x objective. Not all livers were suitable for imaging. Ultimately 1500 images from 30 livers were collected. Each image is a 1388x1040 RGB TIFF with 12 bits of quantization per channel.

Discussion:

AGEMAP images can be analyzed across multiple axis of differentiation: age, gender, diet, or individual mice to construct a variety of classification problems. Classifiers can be trained on livers of the same age and diet to predict the mouse gender. Or similarly trained to predict the mouse diet. Age is a continious variable, so care should be taken when training classifiers to predict mouse age since chornological age doesn't necessarly correspond to morophologcial age.

Staining variability is a major challenge impeding quantitative analysis of H&E slides. All AGEMAP slides that were prepared by the same person, following a set protocol over a short time-period. Thus staining variability in this data-set is significantly lower than staining variabilities in datasets such as the Lymphoma dataset that could not be collected under similarly stringent conditions. It is still very important in your classification experiments to establish that gender/diet/age classifiers are not sensitized to staining varilability and are not exploiting staining to identify mice instead of the appropriate experimental variable.

Experiments:
3 differents subsets of the data were classified using 3 different experiments:
1. Ad-libitum diet female aging: A 4-way classification problem using the four classes of images of female mice on ad-libitum. The classes are 1, 6, 16 and 24 months.
2. 6 months ad-libitum diet gender: A 2-way classifier which classifies the gender of the mouse based on the images of 6-month old male and female mice on ad-libitum diet
3. 6 months caloric restriction diet gender: A 2-way classifier which classifies the gender of the mouse based on the images of 6-month old male and female mice on caloric restriction diet

Female, 6 Months, CR (AMC-112)
Data:

The complete AGEMAP dataset is 12Gb and can downloaded in blocks where each block is several mice from a single age/diet/gender data-point. Click on the links in the table below to download the blocks. The AMC numbers are individual mouse identifiers.

1 month6 months16 months24 months
AL, MaleAMC-141,192AMC-49,87,132AMC-49,87,132AMC-11,38,168
AL, FemaleAMC-145,204AMC-24,94,136AMC-16,47,85AMC-13,14,71
CR, MaleN/AAMC-8,32,63N/AN/A
CR, FemaleN/AAMC-6,35,112AMC-3,95,105N/A