Migrating from ClearMap 2#

ClearMap 3.1 is a substantial redesign of the backend. The GUI is fully backwards-compatible with existing config files (with automatic migration), but scripted workflows need updating.

Concept	ClearMap 2	ClearMap 3.1
Entry point	`ClearMap/Scripts/CellMap.py` `ClearMap/Scripts/TubeMap.py`	`ClearMap/Scripts/cell_map_new_api.py` `ClearMap/Scripts/tube_map_new_api.py`
Processing classes	`TabProcessor` subclasses in `ClearMap.processors`	`PipelineOrchestrator` subclasses in `ClearMap.pipeline_orchestrators`
Workspace	`ClearMap.IO.Workspace` (step-centred)	`Workspace2` (channel-centred, unlimited channels, YAML-persisted)
Config files	`sample_params.cfg`, `cell_map_params.cfg` …	Single `workspace.yml` + per-pipeline YAML files, managed automatically by the GUI or `SampleManager`
Channel support	Fixed two-channel layout (signal + autofluorescence)	Arbitrary number of channels, each with its own data type and pipeline assignment
GPU dependency	Required for vasculature	Required only for deep vessel filling; all other steps are CPU-only
conda environment	`ClearMapUi39`	`ClearMap3.1`

Key API changes#

# ClearMap 2 — direct script execution
# (edit variables at top of CellMap.py and run)

# ClearMap 3.1 — programmatic API
from ClearMap.pipeline_orchestrators.utils import init_sample_manager_and_processors
from ClearMap.pipeline_orchestrators.cell_map import CellDetector

orchestrators = init_sample_manager_and_processors('/path/to/experiment')
sm  = orchestrators['sample_manager']
reg = orchestrators['registration_processor']

for channel in sm.get_channels_by_pipeline('CellMap', as_list=True):
    det = CellDetector(sm, config_coordinator=sm.cfg_coordinator,
                       channel=channel, registration_processor=reg)
    det.run_cell_detection()
    det.post_process_cells()
    det.voxelize()