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Reference atlas creation #63
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In the paper, for drosophila, they use a very extensiv reference atlas from the Berkley lab. Sadly, their data is not available anymore, since they took down their website last year or so. But that wouldn't be helpful anyways, as they put in a lot of effort to manually curate and image thousands of embryos for the marker genes used to get an average spatial expression profile. Then you need to map your expression data on this shape. Eg. measure the proportions and positions of a stripe or area and project that on your previous defined geometry. I would start with binary information, thus assign each location in your target space a 1 if it expresses your gene and a 0 if not. If you have quantitative data, you can of course use a float between 0 and 1 after normalising for all genes. Maybe that helps? Best, Malte |
Hi guys,
I am trying to generate proper files in order to create a reference atlas from antibody staining of genes/TFs in the drosophila optical lobe.
In the paper I did not found any indication about how the dge.txt and the geometry.txt are obtained.
From my understanding I need to generate both, since it is the combination of subset of genes expression x location in the target space.
How are we supposed to generate these files ?
Thank you for your help, and for developing this very useful tool,
Best,
Lilia
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