ClearMap.processors#

Set of classes that each focus on a specific task in the ClearMap pipeline.

The processors are the main building blocks of the ClearMap pipeline. The base class from which all processors inherit is TabProcessor. Then there are 2 types of derived classes, preprocessor and the ones using a preprocessor.

Note batch_process is not a processor but a set of convenience functions to run aspects of: the pipeline on a group of samples.

Sub-packages and modules#

ClearMap.processors.batch_process

The processor set of scripts to batch process a group of samples.

ClearMap.processors.cell_map

This module contains the class to analyze (detect) individual cells, e.g. to analyze immediate early gene expression data from iDISCO+ cleared tissue [Renier2016].

ClearMap.processors.generic_tab_processor

This module contains the generic processor classes that are used to define the processing steps and run the processing This is inherited by all processors in ClearMap

ClearMap.processors.sample_preparation

This is the part that is common to both pipelines to process the raw images.

`ClearMap.processors.batch_process`	The processor set of scripts to batch process a group of samples.
`ClearMap.processors.cell_map`	This module contains the class to analyze (detect) individual cells, e.g. to analyze immediate early gene expression data from iDISCO+ cleared tissue [Renier2016].
`ClearMap.processors.generic_tab_processor`	This module contains the generic processor classes that are used to define the processing steps and run the processing This is inherited by all processors in ClearMap
`ClearMap.processors.sample_preparation`	This is the part that is common to both pipelines to process the raw images.