Archive Meta Data

Author(s)

Jacob Kæstel-Hansen, Marilina de Sautu, Anand Saminathan, Gustavo Scanavachi, Ricardo F. Bango Da Cunha Correia, Annette Juma Nielsen, Sara Vogt Bleshøy, Wouter Boomsma, Tom Kirchhausen, Nikos S. Hatzakis

Title

DeepSPT_Code

Description

Frozen permanent archive containing all code for the paper: 

Minimal working examples can be found in usage_examples python files seen below.

Deep learning assisted single particle tracking for automated correlation between diffusion and function
Jacob Kæstel-Hansen1-4, Marilina de Sautu5,6, Anand Saminathan7-9, Gustavo Scanavachi7-9, Ricardo F. Bango Da Cunha Correia7-9, Annette Juma Nielsen1-4, Sara Vogt Bleshøy1-4, Wouter Boomsma10, Tom Kirchhausen7-9* & Nikos S. Hatzakis1-4* 

See bioarxiv:
doi: https://doi.org/10.1101/2023.11.16.567393
https://www.biorxiv.org/content/10.1101/2023.11.16.567393v1

# DeepSPT
## Deep Learning Assisted Analysis of Single Particle Tracking for Automated Correlation Between Diffusion and Function
DeepSPT, a deep learning framework to interpret the diffusional 2D or 3D temporal behavior of objects in a rapid and efficient manner, agnostically. DeepSPT is a deep learning framework, encompassing three sequentially connected modules: A temporal behavior segmentation module; a diffusional fingerprinting module; and a task-specific downstream classifier module (Fig. 1a). The first two modules are universal, applicable directly to any trajectory dataset characterized by x, y, (z) and t coordinates across diverse biological systems. The final module capitalizes on experimental data to learn a task that is specific to the system under investigation.

![image](_Images/figure1.png)
### Citing
https://www.biorxiv.org/content/10.1101/2023.11.16.567393v1
Check updated status of the publication: https://scholar.google.dk/citations?user=og-0z0wAAAAJ&hl=da

### Usage
#### Installation
DeepSPT's installation guide utilize conda environment setup, therefore either miniconda or anaconda is required to follow the bellow installation guide.
 - Anaconda install guide: [here](https://www.anaconda.com/download)
 - Mini conda install guide: [here](https://docs.conda.io/en/latest/miniconda.html)

DeepSPT is most easily setup in a new conda environment with dependecies, versions, and channels found in environment_droplet.yml or DeepSPT_simple.yml for a simple version of the environemnt file - Open Terminal / Commando prompt at wished location of DeepSPT and run the bash commands below, which creates the environemnt, downloades and installs packages, typically in less than 5 minutes. The code has been tested both on MacOS and Linux operating systems.

```bash
git clone git@github.com:JKaestelHansen/DeepSPT.git OR git clone https://github.com/JKaestelHansen/DeepSPT (potentially substitute JKaestelHansen with hatzakislab
cd DeepSPT
conda env create -f environment_droplet.yml 
conda activate DeepSPT
pip install probfit==1.2.0
pip install iminuit==2.11.0

As second option:
git clone git@github.com:JKaestelHansen/DeepSPT.git OR git clone https://github.com/JKaestelHansen/DeepSPT (potentially substitute JKaestelHansen with hatzakislab
cd DeepSPT
conda env create -f environment_droplet_minimal.yml
conda activate simpleDeepSPT
pip install h5py==2.10.0
pip install imagecodecs==2023.3.16
pip install pomegranate==0.14.8
pip install probfit==1.2.0
pip install iminuit==2.11.0

Note Windows 11 users may need to relax tensorflow-io-gcs-filesystem to require no version

As third option (Thanks to Konstantinos Tsolakidis for contributing approach):
Especially if running this on an Apple Macbook - M1/M2/M3 processor:

git clone git@github.com:JKaestelHansen/DeepSPT.git OR git clone https://github.com/JKaestelHansen/DeepSPT (potentially substitute JKaestelHansen with hatzakislab
cd DeepSPT

conda env create -f DeepSPT_simple.yml 
conda activate DeepSPT
pip install probfit==1.2.0
pip install iminuit==2.11.0

As fourth option (Thanks to Konstantinos Tsolakidis for contributing approach):
Especially if running this on an Apple Macbook - M1/M2/M3 processor:

git clone git@github.com:JKaestelHansen/DeepSPT.git OR git clone https://github.com/JKaestelHansen/DeepSPT (potentially substitute JKaestelHansen with hatzakislab
cd DeepSPT

conda create --name simpleDeepSPT
conda activate simpleDeepSPT
conda install pip

brew install HDF5 (install brew and update path, instructions here: "https://brew.sh/")
(if the above command gives you an issue, run "arch -arm64 brew install hdf5")
export HDF5_DIR=/opt/homebrew/Cellar/hdf5/(1.12.0_4 or your version)
OR 
export HDF5_DIR=/opt/homebrew/opt/hdf5 (if hdf5 is installed in the "/opt/homebrew/opt/hdf5" location, you have to check it out first)
pip install --no-binary=h5py h5py

conda env update --file environment_droplet_minimal.yml

pip install csbdeep==0.7.4
pip install cython==0.29.37
conda install imagecodecs==2023.1.23
pip install pomegranate==0.14.9
pip install probfit==1.2.0
pip install iminuit==2.11.0

Note Windows 11 users may need to relax tensorflow-io-gcs-filesystem to require no version


```
DeepSPT modules and additional/helpful functions are contained in the `deepspt_src` folder.
When running/building scripts in the DeepSPT directory modules are imported as:
```python
from deepspt_src import *

```
Three test python scripts are provided:
  - `simulate_diffusion.py` - Data generation of 2D or 3D diffusion of heterogeneous/homogeneous motion.
  - `usage_example0.py` - Usage example for loading numpy array saved as pickle or csv file.
  - `usage_example1.py` - Usage example for the three DeepSPT modules: Temporal segmentation, diffusional fingerprinting and task-specific classifier module on simulated data. This code transforms trajectories by temporal segmentation of diffusion and provide diffusional fingerprints to generate feature representation of trajectories both in the form of NumPy arrays. Runtime depends on dataset size but runs in less than 10 minutes for typical data volumes.
  - `usage_example2.py` - Usage example for the three DeepSPT modules: Temporal segmentation, diffusional fingerprinting and task-specific classifier module for time-resolved classification on simulated data. This code transforms trajectories by temporal segmentation of diffusion and provide diffusional fingerprints both in a temporal manner and returns the representations in the form of NumPy arrays. Runtime depends on dataset size but runs in less than 10 minutes for typical data volumes.

### For demostration
For demostration regarding presented data and analysis contained in the manuscript, please refer to the `_For_publication` folder where you will find the required information and scripts. To run on the same data download the data as outlined below.

### Data
  - Your own: DeepSPT accepts csv files or numpy arrays of shape (number of tracks, x,y,(z)). The csv files should contain columns named ['x', 'y', 'z', 'particle', 'frame']. Where 'x','y','z' represent coordinates, 'particle' represents particle id (number) and frame represents timepoint (number). The order is not of major importance. For 2D usecases 'z' column should not be included. The numpy arrays inputed as pickle files should have the shape (number of tracks, length of track, 5 or 4) 5 (particle id, frame, x, y, z) for 3D cases and 4 (particle id, frame, x, y) for 2D cases
  - Simulated data: simulate_diffusion.py, usage_example.py, and usage_example2.py (WIP) contains functions to simulate trajectories.
  - To access data of the publication "Deep learning assisted Single Particle Tracking for automated correlation between diffusion and function" please download from: TBA. Please extract .zip files in place of folders with the same names.

### Files
  - For_publication: Scripts as used in "Deep Learning Assisted Analysis of Single Particle Tracking for Automated Correlation Between Diffusion and Function". Folders with data and precomputed files are available, see Data availability.
  - _Images: Contains figure seen in Readme. Copyrighted as detailed in journal carrying "Deep learning assisted Single Particle Tracking for automated correlation between diffusion and function".
  - deepspt_mlflow_utils: MLflow helper functions
  - deepspt_src: Source code for DeepSPT
  - environment_droplet.yml: requirements file for installation of virtual environment.
  - environment_droplet_simple.yml: lighter version of environment_droplet.yml.
  - DeepSPT_simple.yml: a light, easier to install version of the requirements file.

  - Pickle files found in this repo contain arrays of tracks as described in Data section in the Readme. These include both pickle files of trajectories from experimental data and simulated data.
  - Test pickle files for DeepSPT can be found under the _Data folder. The pickle (.pkl) files shape following the above mentioned (see line 81) shape and order.
  

### Runnng on data from publication
- Firstly, download all data as stated in the "Data availability" section in "Deep Learning Assisted Analysis of Single Particle Tracking for Automated Correlation Between Diffusion and Function". Roughly 117 GB in zipped version.
-  Secondly, follow the install instructions described above.
-  Thirdly, the folder "_For_publication" contains all scripts used for the publication and running these will completely reproduce all results. Specifically, temporalsegm_eval.py contains most code for figure 2, timeresolved_uncoating_prediction.py contains most code for figure 3, and benchmark_for_fig4.py contains most code for figure 4.


## Instructions for DeepSPT application - GUI
In this repository you will find the "DeepSPT_GUI_manual.pdf", providing detailed insturcitons on how the applciation of DeepSPT - GUI should be used.
  
### Contact

Jacob Kæstel-hansen, PhD fellow\
Department of Chemistry\
jkh@chem.ku.dk

Konstantinos Tsolakidis,Software Engineer
Department of Chemistry, Hatzakis Lab 
kt@chem.ku.dk

Nikos Hatzakis, Professor\
Department of Chemistry\
hatzakis@chem.ku.dk