Janelia Mouse Atlas

The mouse embryo has long been central to the study of mammalian development. We developed a light-sheet microscope that adapts itself to the dramatic changes in size, shape and optical properties of the post-implantation mouse embryo and captures its development from gastrulation to early organogenesis at the cellular level. We furthermore developed a computational framework for reconstructing long-term cell tracks, cell divisions, dynamic fate maps and maps of tissue morphogenesis across the entire embryo. By jointly analyzing cellular dynamics in multiple embryos registered in space and time, we built a dynamic atlas of post-implantation mouse development that, together with our microscopy and computational methods, is provided as a resource. 

Movies

All movies were encoded using the H.264 video compression standard. They are provided in the form of MPEG-4 files as part of the paper (McDole et al. 2018, Cell), as well as in the form of a combined zip file containing all 28 movies.

Download Movies

Microscope

Free, public access to our adaptive multi-view light-sheet microscope is provided by Janelia's Advanced Imaging Center (AIC).

We furthermore provide a complete blueprint of the adaptive multi-view light-sheet microscope for mouse imaging, including technical drawings of the microscope’s 77 types of custom mechanical components, assembly illustrations for the microscope’s 28 types of multi-part assemblies, and parts list of all custom and commercial mechanical microscope components.

Download Technical Drawings

Software

• Software Module 1: KLB 2.0 block-based lossless image compression file format

• Software Module 2: Block-matching multi-view/time-lapse image registration pipeline

• Software Module 3: GPU-based multi-view image deconvolution software

• Software Module 4: Convolutional neural network for division detection

• Software Module 5: TGMM 2.0 cell tracking framework with machine-learning module

• Software Module 6: Computational framework for Statistical Vector Flow (SVF) analysis

• Software Module 7: Converter for interactive 4D visualization of Statistical Vector Flow (SVF) databases

• Software Module 8: TARDIS framework for spatiotemporal registration of multiple embryos

• Software Module 9: Average embryo database query using external label masks

In addition to the individual software modules listed above, we provide a comprehensive practical software guide with detailed instructions and preconfigured code for all software modules as well as example data.

Download Software Guide (Full Version, 26 GB)

Download Software Guide (Compact Version, 11 GB)

Mouse Atlas

Some of the data sets listed below include large CSV files that are not suitable for opening/browsing with standard editors such as Microsoft Excel or LibreOffice. We recommend opening these data tables in a software environment designed for handling large data structures, such as Python or Matlab.

• Data Set 1: Database of cell tracks with tissue annotations for TARDIS embryo A

• Data Set 2: Database of cell tracks with tissue annotations for TARDIS embryo B

• Data Set 3: Database of cell tracks with tissue annotations for TARDIS embryo C

• Data Set 4: Database of cell tracks with tissue annotations for TARDIS embryo D

• Data Set 5: Interactive visualization of annotated cell tracks for TARDIS embryo A

• Data Set 6: Database of cell divisions for TARDIS embryo A

• Data Set 7: Landmark annotations in the average embryo

• Data Set 8: TARDIS statistical fate map (statistical integration of four embryos)

• Data Set 9: Average embryo (statistical integration of four embryos)

• Data Set 10: Database of tissue morphodynamics for TARDIS embryo A

• Data Set 11: TARDIS database of tissue morphodynamics (statistical integration of four embryos)