docs: updata readme and pipeline howto instructions

Author: cdpaiva

README.md

@@ -1,7 +1,12 @@
 # SNAzzy: an image processing pipeline for investigating global Synchronous Network Activity
 
+SNAzzy is a Python package for studying synchronous network activity (SNA) in Drosophia embryos via high-thoughput microscopy.
+The software includes processing raw data into individual `.tif` files, quantification of fluorescence and changes in morphology, a custom peak detection algorithm, and a GUI for data visualization and curation.
+
 ## Getting Started
 
+Refer to the README files inside the `snazzy_processing` or `snazzy_analysis` packages for details on running the code.
+
 ### Installation
 
 The project uses [conda](https://docs.conda.io) to manage dependencies.
@@ -19,6 +24,18 @@ Activate the environment:
 ```
     conda activate snazzy-env
 ```
+
+## Testing
+
+Tests can be run with pytest.
+
+You can run the test suite from the project’s root directory to test everything at once.
+Make sure the environment is active, and then run:
+
+```
+    pytest
+```
+
 ## Contributing
 
 Thank you for being interested in `snazzy`!

snazzy_processing/notebooks/snazzy-processing-pipeline.ipynb

@@ -8,12 +8,12 @@
     "\n",
     "Integrates all of the modules from the package, to go from raw data to csv output.\n",
     "More information about each module can be found in the other Jupyter Notebooks.\n",
-    "You should change the `dataset name` and the `img_path` at the fist cell.\n",
+    "You should change the `dataset_name` and the `img_path` at the fist cell.\n",
     "\n",
     "If the raw data is in nd2 format, it can be converted directly using the pipeline.\n",
     "For other formats, the image must me converted to tif using another application, for example ImageJ.\n",
     "\n",
-    "Adjust the image paths to where the nd2 file is, and where the tif file will be saved."
+    "Adjust the image path to where the tif/nd2 file is."
    ]
   },
   {
@@ -69,6 +69,8 @@
    "source": [
     "Visualize the regions of the individual embryos that will be cropped.\n",
     "If the bounding boxes don't fit the embryo, you can try changing the `thres_adjust` parameter in `slice_img.calculate_slice_coordinates`.\n",
+    "Decreasing `thres_adjust`, which can be a negative value, tends to generate bigger boxes.\n",
+    "\n",
     "The resulting image also shows the number that will be used for each embryo when saving the individual movies.\n",
     "\n",
     "If after adjust `thres_adjust` the embryos are still not framed as expected, you can use `slice_img.increase_bbox()` to control the bbox dimensions."