---
# System prepended metadata

title: tomogram processing pipeline

---

# tomogram processing pipeline


## components

- on-disk storage
    - all raw and intermediate storage goes in a "file" (e.g., zarr)
- declarative pipeline file
- runner


```yaml=
preprocessing:
  - motion correction
  - ctf estimation
  - tilt-series alignment
  - tomogram reconstruction
 
particle picking:
  - pick the particles (or geometrical supports on which they lie)

refinement:
  - align particles to reference (multiple resolution levels)
  - classification (k-way? continuous?)
  - final reconstruction
  
modelling:
  - post processing of map
  - build model into map
```


## coordinate systems

- multi-frame micrograph (x, y, t)
- micrograph (motion corrected) (x, y)
- tilt-series (x, y)
- tomogram (specimen in 3D) (x, y, z, t)
- structure(s) (intrinsic to reconstructed object) (x, y, z)

## on disk storage


```
my_tomo_project.zarr
    - tilt_series
    - motion_corrected_tilt_series
```


```
motion_correction
 - input: /path/to/raw
 - output: /path/to/mocorr/output
    - my_model
    
reconstruction
 - raw: /path/to/raw
 - model: /path/to/mor/coor/output/my_model



```