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Software Open Access

A high-content imaging method for monitoring C. elegans embryonic development

Wang, Shaohe; Ochoa, Stacy; Khaliullin, Renat; Gerson-Gurwitz, Adina; Hendel, Jeffrey; Zhao, Zhiling; Biggs, Ronald; Chisholm, Andrew; Desai, Arshad; Oegema, Karen; Green, Rebecca

This repository includes the following files:

embryoCropUI_WINDOWS- PC version of executable GUI

embryoCropUI_MacOS- Mac version of executable GUI (requires MacOS X10.11)

Instructions- Instructions for installation and running GUI (embryoCropUI) and FIJI script (OpenAndCombine.ijm)

Test_files- Contains two test files: a multi-tif format file and a folder with a tif image series, which can be used to test the GUI on your system (details for testing can be found in the instructions)

OpenAndCombine_embs.ijm- FIJI script that enables assembly of maximum intensity projections for multiple embryos within one viewer. Note this works with our file structure and will need to be modified to accommodate your file structure (see instructions).

 

source code for the embryoCropUI executable can be found at Github: https://github.com/renatkh/embryo_crop.git
Files (786.7 MB)
Name Size
embryoCropUI_MacOS.zip
md5:adc107a6e302520845d01b156b93a4ff
317.4 MB Download
embryoCropUI_WINDOWS.zip
md5:aaac6ecdd746e01f07693dda352dddf9
350.2 MB Download
GUI_Instructions_zenodo_repo.docx
md5:106fcb58eb56e49609e30d6985cb06a9
1.1 MB Download
OpenAndCombine_embs.ijm
md5:8026d1623d5fb5b5fb88c0d7410970dd
6.6 kB Download
test files.zip
md5:0b8474444e927a4a277e9176dca6f9e0
118.0 MB Download
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