Feature representation of oleaginous yeast images is essential for non-invasively observing their cultivation status. However, conventional methods are difficult to capture the visual characteristics of oleaginous yeasts at the extremely local spatial regions. To tackle this problem, this paper proposes micro-spatial attention with sparse constraints for self-supervised learning. Specifically, we newly design a micro-spatial attention module to focus on the extremely local spatial regions for feature representation. Unlike the existing spatial attention module, which requires the guide information (e.g., labels and textual queries) to focus on specific regions, our proposed module employs a sparse constraint. By combining the sparse constraint with self-supervised learning, we can automatically focus on essential regions, which appear in extremely local regions. This improves the feature representation power for oleaginous yeast images with micro-spatial contexts. Experiments on real Lipomyces starkeyi datasets, a specific type of oleaginous yeasts, confirm the superiority of our method. Moreover, our method realized clustering of oleaginous yeast images, enabling us to non-invasively observe the cultivation trends over time.