Commit 632e0648 authored by Aliaksandr Halavatyi's avatar Aliaksandr Halavatyi
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Update README.md

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# Project description
# General description
Automated Feedback Procedures for the Fly Embryo Screen.
# Experiment setup
Multichamber wide slide with fixed fly embryos stained with 3 dyes:
- DAPI: nuclei
- Alexa488: antibody binds to Ds-red
- Alexa633: antibody for LacZ.
# Contributors
- Timothy Fuqua (Crocker group, EMBL): project runner, main user and tester
- Aliaksandr Halavatyi (ALMF): development and support
# Feedback microscopy protocol:
1. Select manually positions corresponding to the centers of the wells
2. Tile scan overview image with 5x objective.
3. Finding positions of embryos via feedback analysis
4. ...
# Dependencies:
- Fiji
- AutoMicTools library
# Log/updates
See [Documentation](./Documentation/manual.md) for the guidelines
## 2019-03
# Documentation
Version of high-zoom focus job based on `fiji-plugin morphometry` from C. Tischer. It allows split to touching embryos and correctly calculate embryo center in XYZ anfd rotation angle.
Under this [link](./Documentation/manual.md) you will find the detailed description of the tool functions and step-by-step guidelines for the feedback microscopy pipeline.
# Citation
This work is a part of the manuscript:
## ........
> Automated mutagenesis identifies developmental enhancer logic and how it may constrain evolvability
Timothy Fuqua, Jeff Jordan, Marlize van Breugel, Aliaksandr Halavatyi, Christian Tischer, Peter Polidoro, Namiko Abe, Albert Tsai, Chaitanya Rastogi, Richard S. Mann, David L. Stern, Justin Crocker
## 2018-01-05 Tim and Alex
- Configuring acquisition jobs manually.
- Trying feedback experiments with manual selection procedures
- X-Y coordinates are flipping, microscope additionally scans from right to left
\ No newline at end of file
# Contact
Please contact Timothy Fuqua ([timothy.fuqua@embl.de](timothy.fuqua@embl.de)) and Aliaksandr Halavatyi ([aliaksandr.halavatyi@embl.de](aliaksandr.halavatyi@embl.de)) if you have questions, comments or suggestions about using this tool.
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