Maps and atlases are not only visual tools, they are epistemologies. They can help us pay attention to the world using all our senses in order reorientate, navigate and take action as political bodies in an ecological crisis.

Creating an atlas is more encompassing than image acquisition and analysis. It requires a clear understanding of the biological questions to be addressed. Then appropriate labeling, sample preparation, imaging, image analysis, visualization, and data management methods must be selected (Figure 2). An interdisciplinary team is required that collectively possess the needed expertise. Generating useful atlases is still in its infancy. Which methods to use at each step along the pipeline will depend greatly on what analysis is required. There is currently no ‘magic toolbox’ that scientists can use to apply to their specific task. Each step has to be tailored to suit the experiment.

The creation and exploitation of large-scale quantitative atlases will lead to a more precise understanding of development.

The initial inputs for deriving quantitative information of gene expression and embryonic morphology are raw image data, either of fluorescent proteins expressed in live embryos or of stained fluorescent markers in fixed material. These raw images are then analyzed by computational algorithms that extract features, such as cell location, cell shape, and gene product concentration. Ideally, the extracted features are then recorded in a searchable database, an atlas, that researchers from many groups can access. Building a database with quantitative graphical and visualization tools has the advantage of allowing developmental biologists who lack specialized skills in imaging and image analysis to use their knowledge to interrogate and explore the information it contains.

approaches to establish permanent, quantitative datasets—atlases