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* Add to `MultipleDicotPipeline` explanation in notebook

* Cite HackMD in README
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eberrigan authored Apr 5, 2024
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4 changes: 4 additions & 0 deletions README.md
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Expand Up @@ -21,6 +21,10 @@ pip install sleap-roots

## Usage

Detailed trait documentation per pipeline is available here:
[sleap-roots HackMD](https://hackmd.io/DMiXO2kXQhKH8AIIcIy--g)


### `DicotPipeline`

**1. Computing traits for a single plant:**
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12 changes: 8 additions & 4 deletions notebooks/MultipleDicotPipeline.ipynb
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Expand Up @@ -26,10 +26,14 @@
"cell_type": "markdown",
"metadata": {},
"source": [
"The `MultipleDicotPipeline` was constructed for multiple, dicot plants in cylinders with 72 frame image series. \n",
"It expects h5 files, primary and lateral root predictions per cylinder. \n",
"It also expects the number of plants per cylinder in the form of a csv with a column \"number_of_plants_cylinder\" \n",
"for each series in the csv, which should be identified by a column called \"plant_qr_code\". "
"- The `MultipleDicotPipeline` was constructed for multiple, dicot plants in cylinders \n",
"with 72 frame image series. \n",
"- It expects h5 files, primary and lateral root predictions per cylinder. \n",
"- It expects the number of plants per cylinder in the form of a csv with a column \n",
"\"number_of_plants_cylinder\" for each series in the csv, which should be identified by a \n",
"column called \"plant_qr_code\". \n",
"- We also get summary statistics per genotype in this notebook. In order to do this, we \n",
" have a column called \"genotype\" in the input csv."
]
},
{
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