RESOURCES
MOSAIC-lung is an online 3D image viewing website capturing the murine bleomycin-induced lung injury response in Tie2Cre-mTmG mice which enable endothelial cell lineage tracing. The bleomycin model is to date the most commonly used experimental model of lung fibrosis and we were particularly interested in vascular changes during fibrosis and upon resolution. If you are interested in analyzing full image sets from these studies for your own research, please reach out to Brendon (bambren (at) umich (dot) edu).
If you find this resource useful to your research, we ask that you cite the our work establishing this dataset:
ZEBRA is an image analysis pipeline using a combination of the open-source software packages SarcGraph [1, 2] and SarcAsM [3]. This pipeline was created after a qualitative comparison of the outputs from both tools. SarcGraph is first used to preprocess and filter the images, thereby enhancing the visibility of the sarcomeres. The filtered images are then processed with SarcAsM, which generates a binary sarcomere mask. Subsequently, SarcGraph is applied to quantify the total number of sarcomeres, as well as their orientation and length. An additional custom filtering process identifies and counts cell nuclei from DAPI-stained images.
Download all script files at this GitHub link
If you find this resource useful to your research, we ask that you cite the originating papers above and ours:
Jewett et al., Advanced Science, 2026
TRACE is an image analysis pipeline that uses custom Python scripts to analyze calcium transient fluorescence signals from timelapse image sets of commonly use calcium reporter dyes (eg. Cal520, Fluo3/4, Fura-2). The analysis is performed in three sequential steps: First, the image series is registered and warped to the first frame to correct for macroscopic tissue movements, enabling the analysis of fixed regions. Second, a tissue mask and corresponding regions of interest (designated by the user) is generated. Finally, all regional traces are then analyzed for beating synchronicity, beat rate, timing irregularity, calcium rise time, and signal amplitude.
Download all script files at this GitHub link
If you find this resource useful to your research, we ask that you cite our work developing this tool: