DeepTraCe

Instalation

We recoment using a python distribution like Anaconda Python. Trailmap uses Tensorflow 2.1 to segment brains and has been tested with Python 3.7; we include the necessary files for trailmap so no need to install it.

The installation steps assume you have installed Anaconda Python.

Installation steps:

1. clone the git repository: git clone <repository address>
2. go into the repository folder with the terminal and create the conda environement conda env create -f conda-environment.yml
3. run conda activate deeptrace followed by python setup.py develop The first time the package is imported it create a DeepTraCe folder (see below). You'll need to unzip the contents of the models and atlas to the DeepTraCE folder.
4. Download elastix and add it to the path. To add it to the path you can copy the binary files to the conda bin directory - echo $CONDA_PREFIX/bin from a linux/mac terminal or echo %CONDA_PREFIX%\bin from a windows commandline.

Note:

The first time deeptrace is imported, it will create a folder in the user folder called DeepTraCE (i.e. in C:\Users\USERNAME\DeepTraCE on windows, \home\USERNAME\DeepTraCE on linux or \Users\USERNAME\DeepTraCE on mac). You can retrieve the path running import deeptrace;print(deeptrace.utils.deeptrace_path)

The DeepTraCE folder contains:

• DeepTraCE_preferences.json - A file with the paths and preferences
• models - a folder with all the models to be ran in hdf5 format
• registration - a folder with the files required to register the brainbrains to the reference, this will include:
  • average_template_lsfm_10_crop_flip.tif - reference brain
  • annotation_10_lsfm_collapse_crop_flip_newf.nrrd - annotated atlas
  • aba_ontology.csv - table with the region names
  • model_selection.csv - table to select which model gets used for each area

Important Download the models and the atlas from here and unzip it to the DeepTraCE folder.

Analysis steps:

1. Select the stack (we tipically use 2 channels, 488 and 640 - the brains are registered to 488). Load the brains to the BrainStack - as in cell 1.

2. Correct the rotation angles of the brain. When you run the first cell, the 488 stack will be downsampled and opened on a GUI. Use this gui to select 2 locations of the frame that are in the same plane. To do this:

   • find the blood vessels in medial sections and place the mouse over a vessel. Press the z key to mark the first coordinates/plane.
   • Use the slider or the arrows to find a more medial plane that has the same vessel and place the mouse over the same vessel (x and y coords of the vessel are different from the first point). Press the shift z key combination to record the second point.

3. Once the points have been selected, run the second cell. That will run all segmentation models; register the stacks to the average.

4. Run the third cell for combining the models and preparing the resuts.

All results are saved to a folder named deeptrace_analysis one level up from the raw stacks.

Examples in the notebooks folder.