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README.md

SNT Notebooks

This collection of notebooks demonstrates how to access the SNT API from a Python environment.

ℹ️ These instructions were last tested on Ubuntu 22.04 (clean install) on 2022-05-06

Download

To run these notebooks from your local machine, download all the files as a ZIP archive and unzip its contents to a local directory. You can also download the files manually from GitHub. Alternatively, you can clone/fork the entire repository. This may be more advantageous, as you will be able to keep your cloned/forked repository always up-to-date.

Requirements

The core requirement are pyimagej and Fiji.

To Install Fiji:

  1. Download the program.

To install pyimagej:

  1. Install conda. See documentation for details.

  2. Activate the conda-forge channel and set it default:

conda config --add channels conda-forge
conda config --set channel_priority strict
  1. Install pyimagej into a new conda environment named pyimagej:
conda create -n pyimagej pyimagej openjdk

At this point, it is convenient to make the new pyimagej environment available in the graphical notebook interface:

conda install -n pyimagej ipykernel
conda activate pyimagej
python -m ipykernel install --user --name=pyimagej

Now, when you now start jupyter, it will show pyimagej in the list of registered kernels. Selecting it, makes all the packages installed in the pyimagej environment available.

Setup

Before running the notebooks, there are three more things to take care of:

  1. Make sure your Fij installation is up-to-date and subscribed to the NeuroAnatomy update site

  2. Make the notebooks aware of your local Fij.app location. You can do so by editing ijfinder.py:

local_fiji_dir = r'/path/to/your/local/Fiji.app'

(replacing /path/to/your/local/Fiji.app with the actual path to Fiji.app). If you skip this step, you will be prompted to choose the Fiji directory every-time ijfinder.py is called.

  1. If you haven't done so, install the packages required to run these notebooks in the pyimagej environment. The majority requires popular packages available from the default anaconda channel, e.g.:
conda activate pyimagej
conda install pyqt jupyterlab matplotlib pandas seaborn scikit-learn

However, some notebooks require other packages only in conda-forge:

conda activate pyimagej
conda install --channel=conda-forge trimesh

Some functionality may require blender.

Running

Activate the pyimagej environment (if you have not registered it in ipykernel) and start jupyter from the notebooks' directory:

cd /path/to/notebooks/directory
conda activate pyimagej
jupyter notebook

(replacing /path/to/notebooks/directory with the path to the actual directory where you unzipped the notebooks directory).

ℹ️ Some users have reported a jupyter-notebook not found error when calling jupyter notebook from the pyimagej environment. A quick workaround is to use jupyter-lab instead (see details below)

If you prefer JupyterLab (or the 'regular' jupyter-notebook is failing from the pyimagej environment), replace jupyter notebook with jupyter-lab. If not present, you may need to install it on the pyimagej environment:

conda activate pyimagej
conda install jupyterlab
jupyter-lab

Troubleshooting

⚠️ Running SNT from python is pretty much a bleeding edge experience. Things are being actively developed and some things may break. That being said, it is certainly possible (hundreds of people use it frequently). Your feedback is key! Please do reach out if you run into issues.

Installation

If you are having problems setting up your conda environment, it may be useful to ensure your conda is up-to-date:

conda update -n base -c defaults conda

There have been confusing reports of errors related to missing libjvm.so files with java 8 (on Ubuntu 19.10). Adopting a newer openjdk (and pyjnius) seems to fix this:

conda activate pyimagej
conda install openjdk=11

Note that installing packages from multiple channels may lead to conflicts. Packages served by e.g., conda-forge and the regular defaults channel may not be 1000% compatible. You can impose a preference for conda-forge by having it listed on the top of your .condarc file, and by specifying the priority policy, so that packages install from conda-forge by default:

conda config --add channels conda-forge
conda config --set channel_priority strict

Otherwise, you can also use the -c flag to specify a package from a specific channel. E.g., You can install matplotlib from the defaults channel:

conda activate pyimagej
conda install -c defaults matplotlib

or from conda-forge:

conda activate pyimagej
conda install -c conda-forge matplotlib

Converting to/from Java

Certain Java objects returned by SNT may need to be converted to the equivalent Python representation, and vice versa. This is achieved by calling pyimagej's ij.py.from_java() and ij.py.to_java() methods. However, for basic data types such as a Java List, it is possible to cast to a Python list by calling list(). Generally, it is only necessary to use these conversion methods if you run into an error when passing Python data types to Java methods and vice versa. Since pyimagej uses JPype internally, it is often possible to use certain Java objects as if they were Python objects. For example:

>>> from scyjava import jimport
>>> ArrayList = jimport('java.util.ArrayList')
>>> arrayList = ArrayList([1,2,3,4,5])
# Basic slicing is supported
>>> arrayList[:-1]
<java object 'java.util.ArrayList.SubList'>
>>> print(arrayList[:-1])
[1, 2, 3, 4]
# As are certain Python list methods such as append() and extend()
>>> arrayList.extend([6,7])
>>> print(arrayList)
[1, 2, 3, 4, 5, 6, 7]
# However, if we try to stride...
>>> arrayList[::-1]
Traceback (most recent call last):
  File "<stdin>", line 1, in <module>
  File "C:\Users\cam\miniconda3\envs\pyimagej-1.0\lib\site-packages\jpype\_jcollection.py", line 91, in __getitem__
    ndx = _sliceAdjust(ndx, self.size())
  File "C:\Users\cam\miniconda3\envs\pyimagej-1.0\lib\site-packages\jpype\_jcollection.py", line 65, in _sliceAdjust
    raise TypeError("Stride not supported")
TypeError: Stride not supported
# Nonetheless, we can simply cast to a Python list with list()
>>> list(arrayList)[::-1]
[7, 6, 5, 4, 3, 2, 1]

For more details have a look at the SNT and pyimagej introductory notebooks.

Resources

SNT pyimagej
Documentation Documentation
API Getting Started
Source code Source code
Image.sc Forum Image.sc Forum