vidtrain 0.1.0

Deep learning annotation training and prediction workflow for microscopy video data

VidTrain

Train deep neural networks to analyze video data.

Installation

1. Install anaconda
2. (Optional) Install a python-capable IDE like Visual Studio Code
3. Open a command line terminal to install vidtrain:
   1. Create a python 3.7 environment: conda create --name vidtrain python=3.7. Note, the python version must be exactly 3.7 [1]
   2. Activate the environment conda activate vidtrain
   3. Install vidtrain pip install vidtrain

Notes

[1] The code uses some features that were introduced in 3.7 (dictionaries that are ordered by default), meaning it will not work properly with python <3.7. Furthermore, it uses Tensorflow 1 , which dpes not support 3.8. Thus, the python version must be exactly 3.7. In the future, it is planned to migrate to Tensorflow 2 and at that point, vidtrain will also work on python 3.8. However, this will require rewriting at least the data generator for the validation data.