Prepare Batch Projects

Prepare a batch project from tomograms

New in v1.0.3

If you are going to analyze many tomograms, it is convenient to prepare a batch project first. It is simply easier to manage your data with a batch project; you can open each project one by one in the batch analyzer widget, with consistent parameters.

Batch open

Example 1: Prepare a batch project from IMOD projects

After tomogram reconstruction using IMOD, you will have directories like below:

data/
  ├─ TS_01/
  │   ├─ TS_01.mrc
  │   ├─ TS_01_rec.mrc
  │   └─ ...
  ├─ TS_02/
  │   ├─ TS_02.mrc
  │   ├─ TS_02_rec.mrc
  │   └─ ...
  ├─ TS_03/
  │   └─ ...
  └─ ...

Under the data/ directory, first prepare a .cylindra-defaults.toml file to configure the default parameters for reading each tomogram:

cylindra prep-defaults

and edit the generated file:

vim .cylindra-defaults.toml

Following setting means that the tomogram contrast will be inverted, 2x and 4x binned tomograms will be calculated on loading the tomogram, and the "Lowpass" filter will be applied to the reference image (in this case, 4x binned tomogram).

.cylindra-defaults.toml

invert = true
bin_size = [2, 4]
filter = "Lowpass"

This defaults will be referred when preparing a batch project using following command:

cylindra prep "TS_*/*_rec.mrc" myprojects

This command will prepare a batch project under myprojects/ directory, with individual project files.

data/
  └─ myprojects/
      ├─ TS_01
      │   ├─ project.json
      │   └─ script.py
      ├─ TS_02
      │   ├─ project.json
      │   └─ script.py
      :
      ├─ project.json
      └─ script.py

List of patterns

You can pass multiple patterns separated by semicolons (;):

cylindra prep "project_001/TS_*/*_rec.mrc;project_002/TS_*/*_rec.mrc" myprojects

The created batch project can be opened by the following command:

cylindra open myprojects
# or
# cylindra open myprojects/project.json

Example 2: Link denoised tomograms

You may have binned and denoised tomograms already, organized like below:

data/
  ├─ TS_01/
  │   ├─ TS_01_rec.mrc
  │   ├─ TS_01_rec_denoised.mrc
  │   └─ ...
  ├─ TS_02/
  │   ├─ TS_02_rec.mrc
  │   ├─ TS_01_rec_denoised.mrc
  │   └─ ...
  ├─ TS_03/
  │   └─ ...
  └─ ...

As mentioned here, you can specify denoised tomograms as the reference images to improve visualization and particle picking. To link TS_XX_rec_denoised.mrc as the reference image of TS_XX_rec.mrc, set the image_reference entry in the .cylindra-defaults.toml file like below:

.cylindra-defaults.toml

image_reference = "{}_denoised.mrc"

{} is the placeholder for the tomogram path without extension. This value will be evaluated for each tomogram.

Batch project can be opened with the same command:

cylindra prep "TS_*/*_rec.mrc" myprojects

Example 3: Prepare a batch project from existing `cylindra` projects

You can pass a pattern of existing cylindra project files instead of tomogram files to the cylindra prep command.

cylindra prep "projects_251029/TS_*" myprojects

Make a batch project in GUI

You can make a batch project by adding existing cylindra projects one by one in GUI. From the menu bar of the batch analyzer widget, click File > Add projects.