Automatic Morphological Analysis of Podocytes (AMAP) - method for segmentation and morphology quantification of fluorescent mocroscopy images of podocytes https://www.biorxiv.org/content/10.1101/2021.06.14.448284v3
- Installation
Inference uses BICO method to accelerate the clustering. bico_source contains the source code that you need to compile next copy BICO executable and CluE library to a folder bico next to the amap folder. The folder hierarchy should look as follows:
./amap
|---amap
|---bico
| |---BICO_Experiments
| |---BICO_Quickstart
| |---cluster
| |---libCluE.a
|---bico_source
|---sample_images
- Generation of train data
Running training requires binarized image and label files that can be efficiently used through the training iterations. We provide a set of sample images and their binar labels in the sample_images folder. Running
python generate_data.py
with default arguments will convert the images in the sample_images folder into the binary format and place them in a data folder.
- Training
Training can be performed on cpu or a given number of gpus, defined by the -g parameter. -g 0 will perform the training on the cpu. For example
python train_amap.py -g 2
will use 2 gpus in training.
By default training set will be located in the data folder and checkpoints saved in the checkpoints folder according to such a folder structure:
./amap
|---amap
|---bico
|---bico_source
|---checkpoints
|---data
| |---test
|---sample_images
with test dataset in the data/test folder. These parameters can be also passed as stript arguments -dd and -dc respectively.
- Inference
The same -g parameter will define the device for inference. Depending on your compute capacity modify variables in the amap_predict.py script and adapt NPROC_TILE and NPROC_CLUSTER variables. These variables define the number of processes that will postprocess the segmentation results.
By default images are read from sample_images folder and results saved in amap_res folder. You can change these with -i and -o parameters respectively.
- Morphometric parameters
Calling
python3 morphometry.py
will infer morphometric parameters on files in the folders set as default:
- images
-i ../sample_images - segmentation results
-p ../amap_res - output folder
-o ../amap_res/morphometry
This script estimate individuals foot process parameters, slit diaphragm parameters, and joint results that are saved in the output folder as all_params.xls file. Results of each step are saved in the same folder.