ClearMap API#
ClearMap is a toolbox for the analysis and registration of volumetric data.
It has been designed to analyze O(TB) 3D datasets obtained
via light sheet microscopy from iDISCO+ cleared tissue samples
immunolabeled for proteins.
ClearMap includes * non-rigid wobbly stitching, * image registration to a 3D annotated references (e.g. the Allen Brain Institute Atlases), * a toolbox for large volumetric image processing O(TB), * object and cell detection, * vasculature detection and graph construction, * statistical analysis
ClearMap has been written for mapping immediate early genes [Renier2016]
as well as vasculature networks of whole mouse brains [Kirst2020].
This tools may also be useful for data obtained with other types of microscopes, types of markers, clearing techniques, as well as other species, organs, or samples.
ClearMap is written in Python 3 and is
designed to take advantage of
parallel processing capabilities of modern workstations. We hope the open
structure of the code will enable many new modules to be added to ClearMap to
broaden the range of applications to different types of biological objects or
structures.
More information and downloads for ClearMap can be found in our repository.
This sub-package handles stitching and alignment of volumetric data. |
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ClearMap analysis and statistics toolbox. |
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This module handels data reading and writing in ClearMap via sources and sinks. |
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This sub-package provides routines for volumetric image processing in parallel |
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This sub-package provides functions for parallel processing of data for ClearMap. |
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Folder containing the main processing pipeline scripts. |
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Module to set ClearMap's internal parameter and paths to external programs. |
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Utility functions used throughout ClearMap. |
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This sub-package provides tools for the visualization of the data and analysis results using the vispy library. |
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This subpackage handles the text configuration files for ClearMap. |
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This subpackage contains the graphical user interface for ClearMap. |
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Set of classes that each focus on a specific task in the ClearMap pipeline. |