Commit 76c50dd3 authored by Christoph Sommer's avatar Christoph Sommer

initial notebook inline docu

parent 8e1935ac
......@@ -6,7 +6,23 @@
"source": [
"# CARE user interface\n",
"---\n",
"Use SHIFT+ENTER to step through the code cells"
"#### Usage\n",
"\n",
"A **code cell** will either:\n",
"* import required modules\n",
"* produce GUI elements for setting parameters or input files\n",
"* execute a CARE processing step\n",
"* an execution is finished, when the *****-symbol left of the code cell disappears\n",
"\n",
"Use **SHIFT+ENTER** to execute the selected code cell and step through the notebook\n",
"\n",
"#### Background\n",
"* CARE requires perfectly alligned pairs of low and high quality images for training. The low quality image can have a by a factor of 2 lower resoltion. \n",
"* After training, new, low quality images can be predicted with the trained model.\n",
"* Input images will be loaded with the Bioformats library (supports e. g. tif, czi, lsm, etc.)\n",
"* 2D, 3D and movies are supported.\n",
"* Each channel will be processed independently\n",
"* For more information visit the [BIF_CARE](https://github.com/sommerc/bif_care) or the [CARE](http://csbdeep.bioimagecomputing.com/) webpage"
]
},
{
......@@ -112,7 +128,9 @@
"metadata": {},
"source": [
"## 4. Prediction\n",
"---"
"---\n",
"**requires loaded and trained project**\n",
"* Images will be tiled according to the **n_tiles** (z,y,x) parameter. (usefull for big images)"
]
},
{
......@@ -130,7 +148,7 @@
"metadata": {},
"outputs": [],
"source": [
"BifCareTrainer(**gui.params).predict_multiple(predict_file.value, n_tiles=(1,1,1))"
"BifCareTrainer(**gui.params).predict_multiple(predict_file.value, n_tiles=(1,4,4))"
]
},
{
......
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