interactive-render-workflow

Interactive workflow for aligning volume electron microscopy datasets derived from FAST-EM, making use of render-ws. This software is being used to reconstruct FAST-EM array tomography datasets as described in Kievits et al. (2024). The software performs interactive post-correction of FAST-EM image data, import to render-ws, 2D stitching, 3D alignment and export to WebKnossos.

The following is currently supported:

• Post-correction of FAST-EM image data
• Import to render-ws
• 2D stitching
• 3D alignment
• Export to local WebKnossos instances

Requirements

• Server with Linux distribution (Ubutuntu) and decent computation power (>128 GB RAM, >40 CPU cores).
• render-ws installation (setup instructions)
• Local WebKnossos instance (setup instructions). Since we are using a self-hosted WebKnossos instance, export to the Remote WebKnossos is currently not supported be can be considered on request.
• scripted-render-pipeline installation

Installation

It is recommended to install interactive-render-workflow in a Python virtual environment or with help of a Python environment manager such as Conda or Mamba, to prevent changes to your system Python installation.

Instructions for venv (Python virtual environment, requires Python3.10 installation)

python3 -m venv /path/to/new/virtual/environment

Activate environment:

source /path/to/new/virtual/environment/bin/activate

Install repository

pip install git+https://github.com/hoogenboom-group/interactive-render-workflow.git

Clone BigFeta into a suitable directory (required for alignment scripts)

git clone https://github.com/AllenInstitute/BigFeta/

Usage

The usage is covered entirely by JuPyter Notebooks:

1. post-correct.ipynb is for optimizing post-correction for a single section and then applying these settings to all sections
2. import.ipynb is for import to render-ws
3. stitch_render-client.ipynb uses the render-ws routines to perform in-plane (2D) alignment (stitching)
4. rough_align_render-client.ipynb performs rough alignment (as input to the final fine alignemnt step)
5. fine_align_render-client.ipynb performs the fine alignment
6. export.ipynb performs export of 3D aligned stacks to WebKnossos

We are currently writing routines to perform stitching and alignment using alternative feature-finding algorithm implementations (stitch.ipynb, align.ipynb). These are still under construction.

License

Licensed under the GNU Public license, Version 3.0 (the "License"); you may not use this software except in compliance with the License.

Unless required by applicable law or agreed to in writing, software distributed under the License is distributed on an "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. See the License for the specific language governing permissions and limitations under the License.

Support

This code is an important part of the Hoogenboom group code base and we are actively using and maintaining it. This means that the documentation and API may be subject to changes. Issues are encouraged, but this software is released with no fixed update schedule.