mousemorph | Tools for MRI mouse brain morphometry | Data Labeling library

by nmpowell Python Version: Current License: BSD-3-Clause

X-Ray Key Features Code Snippets Community Discussions(3)Vulnerabilities Install Support

kandi X-RAY | mousemorph Summary

mousemorph is a Python library typically used in Healthcare, Pharma, Life Sciences, Artificial Intelligence, Data Labeling applications. mousemorph has no bugs, it has no vulnerabilities, it has a Permissive License and it has low support. However mousemorph build file is not available. You can download it from GitHub.

Tools for MRI mouse brain morphometry. MouseMorph is a modular set of tools for automatically analysing mouse brain MRI scans. It enables fully automatic [Voxel- and Tensor-Based Morphometry][ashb_vbm_2000] (VBM, TBM) on large cohorts of high-resolution images. It is employed at the UCL Centre for Advanced Biomedical Imaging ([CABI][CABI]) for [phenotyping] mice based on in vivo and ex vivo MRI. It has been tested for robustness on hundreds of mouse brain scans. The primary distinction from clinically-focussed tools like [SPM] and [FSL] is a robust set of pre-processing steps, unique to — or with customisations for — the preclinical paradigm (mice and rats): - Identification and extraction of multiple subjects from a single scan image - Orientation to a standard space, from any initial orientation - Mouse brain extraction (skull stripping / brain masking) - Tissue segmentation, using accurate, mouse-specific priors - Group-wise registration.

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mousemorph has a low active ecosystem.

It has 20 star(s) with 8 fork(s). There are 2 watchers for this library.

It had no major release in the last 6 months.

There are 2 open issues and 0 have been closed. On average issues are closed in 862 days. There are no pull requests.

It has a neutral sentiment in the developer community.

The latest version of mousemorph is current.

Quality

mousemorph has 0 bugs and 0 code smells.

Security

mousemorph has no vulnerabilities reported, and its dependent libraries have no vulnerabilities reported.

mousemorph code analysis shows 0 unresolved vulnerabilities.

There are 0 security hotspots that need review.

License

mousemorph is licensed under the BSD-3-Clause License. This license is Permissive.

Permissive licenses have the least restrictions, and you can use them in most projects.

Reuse

mousemorph releases are not available. You will need to build from source code and install.

mousemorph has no build file. You will be need to create the build yourself to build the component from source.

Installation instructions are available. Examples and code snippets are not available.

mousemorph saves you 1131 person hours of effort in developing the same functionality from scratch.

It has 2556 lines of code, 185 functions and 6 files.

It has high code complexity. Code complexity directly impacts maintainability of the code.

Top functions reviewed by kandi - BETA

kandi has reviewed mousemorph and discovered the below as its top functions. This is intended to give you an instant insight into mousemorph implemented functionality, and help decide if they suit your requirements.

Go to the specified location .
Calculate the convex hull of a binary image .
Sanitise arguments .
Crop the image .
Loop through a list of files .
Register and compare calibration and reference images .
Label connected components .
Scale data volume by a given percentage .
Check if a csv file exists .
Corrects the distortion offset .

Get all kandi verified functions for this library.

mousemorph Key Features

No Key Features are available at this moment for mousemorph.

mousemorph Examples and Code Snippets

No Code Snippets are available at this moment for mousemorph.

Community Discussions

Trending Discussions on Data Labeling

How can I do this split process in Python?

Replacing a character with a space and dividing the string into two words in R

Azure ML FileDataset registers, but cannot be accessed for Data Labeling project

QUESTION

How can I do this split process in Python?

Asked 2021-Dec-30 at 14:06

I'm trying to make a data labeling in a table, and I need to do it in such a way that, in each row, the index is repeated, however, that in each column there is another Enum class.

What I've done so far is make this representation with the same enumerator class.

A solution using the column separately as a list would also be possible. But what would be the best way to resolve this?

...

ANSWER

Answered 2021-Dec-30 at 13:57

Instead of using Enum you can use a dict mapping. You can avoid loops if you flatten your dataframe:

Source https://stackoverflow.com/questions/70532286

QUESTION

Replacing a character with a space and dividing the string into two words in R

Asked 2020-Nov-18 at 07:32

I have a dataframe that contains a column that includes strings separeted with semi-colons and it is followed by a space. But unfortunately in some of the strings there is a semi-colon that is not followed by a space.

In this case, This is what i'd like to do: If there is a space after the semi-colon we do not need a change. However if there are letters before and after the semi-colon, we should change semi-colon with space

i have this:

...

ANSWER

Answered 2020-Nov-16 at 07:24

Try something like:

Source https://stackoverflow.com/questions/64853962

QUESTION

Azure ML FileDataset registers, but cannot be accessed for Data Labeling project

Asked 2020-Oct-28 at 20:31

Objective: Generate a down-sampled FileDataset using random sampling from a larger FileDataset to be used in a Data Labeling project.

Details: I have a large FileDataset containing millions of images. Each filename contains details about the 'section' it was taken from. A section may contain thousands of images. I want to randomly select a specific number of sections and all the images associated with those sections. Then register the sample as a new dataset.

Please note that the code below is not a direct copy and paste as there are elements such as filepaths and variables that have been renamed for confidentiality reasons.

...

ANSWER

Answered 2020-Oct-27 at 22:39

Is the data behind virtual network by any chance?

Source https://stackoverflow.com/questions/64546521

Community Discussions, Code Snippets contain sources that include Stack Exchange Network

Vulnerabilities

No vulnerabilities reported

Install mousemorph

Download, and install, [NiftyReg], and [NiftySeg]. Ensure the executables are on your system path ([Linux](http://www.computerhope.com/issues/ch001647.htm); [Windows](http://www.computerhope.com/issues/ch000549.htm)). You need at least Python 2.7. Try [Anaconda], which includes the required NumPy, SciPy, Pandas, Matplotlib. You also need [NiBabel]. From a command line, run: pip install nibabel. [Download the MouseMorph repository as a .zip](https://github.com/nmpowell/mousemorph/archive/master.zip), and extract. From the mousemorph directory, run: python setup.py install.
Download, and install, [NiftyReg], and [NiftySeg]. Ensure the executables are on your system path ([Linux](http://www.computerhope.com/issues/ch001647.htm); [Windows](http://www.computerhope.com/issues/ch000549.htm))
You need at least Python 2.7. Try [Anaconda], which includes the required NumPy, SciPy, Pandas, Matplotlib.
You also need [NiBabel]. From a command line, run: pip install nibabel
[Download the MouseMorph repository as a .zip](https://github.com/nmpowell/mousemorph/archive/master.zip), and extract
From the mousemorph directory, run: python setup.py install