理解腦的運作是本世紀人類科學重要的疆界之一，其中最關鍵的困難點在於無法觀察到腦中的「軟體」，也就是腦中所有的神經元連結所造成的突現性質 (emergent property) 或資訊流。我們提出的做法是發展光學影像技術，擷取活體全腦中每個神經乃至突觸之間的信號流動，以反推軟體運作。在這篇文章中，我介紹三項我們最近發展的相關技術突破，包括成功實現在果蠅腦中的高速體積雙光子影像系統，可以用毫秒級時間解析度觀察神經之間的動態連結。進一步結合精準光學刺激與光遺傳技術，實現高速體積全光學生理操控與觀察；還有結合共軛焦技術、組織澄清、以及局域化定位超解析技術在全果蠅腦中可達 20 奈米超高空間解析度等。這些創新技術不僅讓我們有機會觀察完整活體小動物腦的反應，未來也有機會應用在其他不同的生物醫學研究領域上。

To understand how brain functions is the grand scientific challenge of 21st century. Brain is composed of millions of neurons, whose interconnection, i.e. connectome, determines its function. Although the interaction of neurons in vitro has been well studied in the past century, the major bottleneck is that no existing tool can capture whole-brain in vivo emergent properties at single neuron or even synapse resolution. To understand functional connectome, an imaging system that can cover a whole living brain with spatial resolution of micrometers (neuron) to nanometers (synapse) as well as temporal resolution in sub-seconds (calcium) to milliseconds (action potential) is highly desirable. In this review article, I introduce our recent efforts to improve optical microscopy in terms of speed and resolution, toward the goal of understanding the brain of Drosophila, which offers a small brain with sophisticated functions and genetic control capabilities. By pushing the limits of optical microscopy, these novel techniques will benefit not only brain science, but also studies in other biomedical researches.