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IMOD

Introduction

IMOD is a suite of modelling, display and image processing programs for 3D reconstruction of electron microscopy and optical sections. It has a long history, being developed primarily by researchers at the University of Colorado since 1994.

Using IMOD

Prerequisites: IMOD provides a range of command-line and GUI-based programs. It can be run without a GPU, but GPU acceleration is recommended for many processing tasks such as tomogram reconstruction an alignment. GPU support requires an NVIDIA card with drivers supporting CUDA 12.0 or later (most modern cards).

We cover how to run the containers and a practical example using the 3dmod executable. Detailed instructions for the large number of tools IMOD provides can be found in the IMOD user manual.

Running the Container

Due to the large number of IMOD components to chose from, the recommended way to use the RFI IMOD container is to start a shell (bash) session inside the container, from which all IMOD programs are available.

In Apptainer, this is done using 

apptainer shell --nv docker://quay.io/rosalindfranklininstitute/imod-container
If you don't have a NVIDIA GPU, omit the --nv option.

A list of available IMOD programs can then be found by entering 

ls $IMOD_DIR/bin
All of these commands are available from the command line within the container. For example, 3dmod will launch the 3dmod program and etomo will launch the etomo program.

For the equivalent in Docker, first enable containers to access the host display by running xhost +local: (or xhost + for a remote host). Then run: 

docker run -it  \
   --gpus all \
   -e DISPLAY=$DISPLAY \
   -v /tmp/.X11-unix:/tmp/.X11-unix \
   --device=/dev/dri:/dev/dri \
   quay.io/rosalindfranklininstitute/imod-container \
   bash
Where you can omit the --gpus all flag if you don't have a NVIDIA GPU.

To mount additional data directories e.g. a network drive, add --bind /path/to/files:/mnt in Apptainer or -v /path/to/files:/mnt. Here /path/to/files is a location on your machine and /mnt where the data will appear in the container.

Starting with 3dmod

3dmod is IMOD's visualisation and modelling program and for many the primary component of IMOD they will use. 3dmod primarily works with MRC files, which are a standard format for storing 3D image data in electron microscopy, but can also open individual TIFF images.

Enter 3dmod in the container terminal window to start the application:

3dmod Startup

For a test example, you can download the sample dataset provided the University of Colorado: imod_data.tar.gz. Unzip this and use Select in the 3dmod image to select one of the example .mrc files. Pressing OK launches the main 3dmod program.

3dmod Example

The information window on the left is the main point of control and information when working with model data. The image display on the right can be panned and zoomed using the mouse with toolbar options to perform annotations. A complete tutorial for using these functions can be found on the University's Introduction to 3dmod. Another helpful resource is Andrew Noske's IMOD Wiki.

Tip

The tif2mrc tool can be used to convert a sequence of .tiff files into a .mrc file.

Troubleshooting and Support

Getting help

We are currently working with users to determine potential issues with the IMOD container and steps to resolve them.

If you encounter problems with the IMOD container, Create an issue on the container GitHub repository. Please share as much information as you can regarding your host system (operating system, container runtime), the commands you are trying to run as well as any error messages.

Version and license information

The container provides IMOD 5.1.2 with CUDA 12.0. It is distributed under an Apache 2.0 License. Bibliographic information for IMOD can be found on the IMOD Home Page.