Installation

This is a preliminary installation instruction. This may not work on all systems. If any problems come up, do not hesitate to contact us rkiewisz@nysbc.org, or contact us on our Slack Channel.

We are working on a more intuitive installation of our software. In the meantime please use the following options.

Option 1:

Install TARDIS using the newest released package from Github

pip install package_name-py3-none-any.whl

or

or

And jump to Validate.

Option 2:

Build a package from the source

Step 1: Clone repository

git clone https://github.com/SMLC-NYSBC/TARDIS.git

Step 2: Create a conda environment

Before starting, it is beneficial to create a virtual Python environment. In these cases, we use Miniconda.

If you don’t know if you have installed Miniconda on your machine, please run:

conda -h

If you don’t have Miniconda, you could install it following official instruction.

Now you can create a new conda environment:

conda create -n <env_name> python=3.11

And to use it, you need to active it:

conda activate <env_name>

Step 3: Install TARDIS

The following command will install TARDIS and all its dependencies

pip install tardis-em

or

conda install tardis-em

(Optional) Install from GitHub master branch:

cd TARDIS
pip install .

Validate installation

To check if the installation was successful and check for any new OTA updates, you can run:

tardis

This should display the TARDIS home screen, similar to the screenshot below:

_images/main_tardis.jpg

[Optional] installation of Napari plugin

pip install napari-tardis-em

Run automatic segmentation

  • Advance Tutorial - Predict Microtubules in 3D [Tutorial].

tardis_mt -dir path/to/folder/with/your/tomograms

  • Advance Tutorial - Predict Microtubules in 2D [Coming soon] [Tutorial]

TBD

  • Advance Tutorial - Predict Membrane in 3D [Tutorial]

tardis_mem -dir path/to/folder/with/your/tomograms

  • Advance Tutorial - Predict Membrane in 2D [Tutorial]

tardis_mem2d -dir path/to/folder/with/your/tomograms