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Recent Releases of Brainchop

Brainchop - brainchop-v4.1.0

In v4.1.0, following fixes has been added :

  • Fix brainchop parameters (b3372b8)

  • Fix 104 high memory and fast model parameter (e36437a)

  • Cleaning code (e.g. 1fc13a0).

Scientific Software - Peer-reviewed - JavaScript
Published by Mmasoud1 almost 2 years ago

Brainchop - brainchop-v4.0.0

Release Notes

Version 4.0.0

We are thrilled to welcome Chris Rorden (@neurolabusc) and Taylor Hanayik (@hanayik) as new contributors to brainchop. Special thanks to them for their main contributions to version 4. (67396d2).

Release supervision: @sergeyplis

Merging and configuration: @Mmasoud1

New Features

  • Integration of the NiiVue viewer for loading and visualization. This allows drag and drop support for voxel formats including NIfTI, NRRD, MRtrix MIF, AFNI HEAD/BRIK, MGH/MGZ, ITK MHD, ECAT7 as well as limited DICOM support.

  • Allows models to be run either on the main thread (as before) or a web worker

  • Allows classifications to be edited by drawing to append or erase voxels.

  • Allows entires scenes (images, classification results, contrast, crosshair position, drawings) to be saved as NiiVue documents that can be opened anywhere.

Enhancements

  • Refactoring for improved performance
  • Optimized pre and post-processing steps
  • Removes the Python dependencies (pyodide) for the conform function, and replaces this function with native JavaScript.
  • Reduces static memory usage.
  • Dramatically reduces peak heap memory usage (for low memory 104 region model the reduction is x173).

Scientific Software - Peer-reviewed - JavaScript
Published by Mmasoud1 about 2 years ago

Brainchop - brainchop-v3.4.0

In v3.4.0, following fixes has been added :

  • 2x speedup for sequential low memory models (2e555f4)

Scientific Software - Peer-reviewed - JavaScript
Published by Mmasoud1 about 2 years ago

Brainchop - brainchop-v3.3.0

In v3.3.0, following fixes has been added :

  • Accelerate connected components post processing (89a01c9)

Scientific Software - Peer-reviewed - JavaScript
Published by Mmasoud1 about 2 years ago

Brainchop - brainchop-v3.2.1

In v3.2.1, following fixes has been added : - Fix buffer leakage (03d4019)

  • Fix Normalization issue #22 (b17d9c6)

Scientific Software - Peer-reviewed - JavaScript
Published by Mmasoud1 about 2 years ago

Brainchop - brainchop-v3.2.0

In v3.2.0, following features and fixes has been added : - Add new failsafe subcortical model use preModel for cropping (0fe66a3)

  • Activate production mode (0fe66a3)

  • Turn on enableCrop for light model (0fe66a3)

Scientific Software - Peer-reviewed - JavaScript
Published by Mmasoud1 about 2 years ago

Brainchop - brainchop-v3.1.0

In v3.1.0, following fixes has been added : #### Fixes

  • Fixed 3D connected components bug with textures f16 bits (eff81f3)

  • Turn off preModel cropping for Sub-cortical models (71a1a49)

Scientific Software - Peer-reviewed - JavaScript
Published by Mmasoud1 about 2 years ago

Brainchop - brainchop-v3.0.0

In v3.0.0, we added the following features : #### Features:

  • Add more robust models (2b061eb)

  • Add Pytorch to TFJS conversion example (7840eec)

Scientific Software - Peer-reviewed - JavaScript
Published by Mmasoud1 about 2 years ago

Brainchop - brainchop-v2.4.0

In v2.4.0, we add more options : #### Features:

Scientific Software - Peer-reviewed - JavaScript
Published by Mmasoud1 about 2 years ago

Brainchop - brainchop-v2.3.0

In v2.3.0, we add more options and addressed the following fixes : #### Fixes:

  • Fix memory (baa236b)

  • Add sequential convolution option for low memory resources (1c4f657)

Scientific Software - Peer-reviewed - JavaScript
Published by Mmasoud1 about 2 years ago

Brainchop - brainchop-v2.2.0

In v2.2.0, we addressed the following minor fixes and adding a Colab example for DL training:

#### Fixes:

  • Fix .nii extension with mri_convert (fb8cccb)

  • Add Colab Example for MeshNet training (87a1ba9)

  • Fix unit testing links (441f5be)

Scientific Software - Peer-reviewed - JavaScript
Published by Mmasoud1 over 2 years ago

Brainchop - brainchop-v2.1.0

In v2.1.0, we addressed the rest of JOSS reviewers reported bugs in addition to those addressed in v2.0.1.

#### Fixes:

  • Adjusted padding to fix Papaya MRI viewers planes visibility for screens of width > 1350 (1c9f924).

  • Added two deeper Meshnet models for better brain extraction and masking accuracy (0c6f90e).

  • Fixed Mocha testing for normalizeVolumeData function (60c2240).

  • Modified info and warning messages text (be8e0a8).

Scientific Software - Peer-reviewed - JavaScript
Published by Mmasoud1 about 3 years ago

Brainchop - brainchop-v2.0.1

#### Fixes:

  • ِِAdd scrollbar to the left mini forms container (e951fbd) (#18 )

  • Fix models info and warning tooltips (9f5cae7) (#19 )

Scientific Software - Peer-reviewed - JavaScript
Published by Mmasoud1 about 3 years ago

Brainchop - brainchop-v2.0.0

With v2.0.0, it can be said that brainchop in a relatively short time exceeded the expectations as the first front-end neuroimaging tool for volumetric MRI processing. Many features have been added to brainchop functionality since first version to support data residency, 3D data rendering, preprocessing, volumetric segmentation, and postprocessing for the first time in the browser. We hope that proof of concept will pave the road for next-generation neuroimaging applications in the browser.

#### Features:

  • Add Mocha unit testing (accac1f).

  • Create draft-pdf yml file. (a3f88e3).

  • Add check browser resources option. (b877464).

  • Add list of verified H/W and S/W. (b877464).

Scientific Software - Peer-reviewed - JavaScript
Published by Mmasoud1 over 3 years ago

Brainchop - brainchop-v1.4.0

#### Features:

  • Add 3D real-time rendering of the input Nifty file. (44485e8).

  • Add 3D Image processing algorithms for input denoising and enhancing. (44485e8).

Scientific Software - Peer-reviewed - JavaScript
Published by Mmasoud1 over 3 years ago

Brainchop - brainchop-v1.3.0

#### Features:

  • Add three.js with WebGL backend to support T1 MRI rendering and filtering regions of interest in real time. (a2c9842).

  • Create three.js dat.GUI checkbox list extension to support selecting multiple segmented region to 3D visualization. (f76eee2).

  • Add bar chart to plot Meshnet segmentation output volumes. (a2c9842).

  • Adjust layout to add new options.(a2c9842)

Scientific Software - Peer-reviewed - JavaScript
Published by Mmasoud1 almost 4 years ago

Brainchop - brainchop-v1.2.1

#### Fixes:

  • Fix environment parameters (2cfc9d7).

Scientific Software - Peer-reviewed - JavaScript
Published by Mmasoud1 almost 4 years ago

Brainchop - brainchop-v1.2.0

#### Features:

  • Add 50 segmentation model to segment MRI cortical regions. Each cortical structure region is marked with a unique color/label compatible with FreeSurfer (8375a08).
  • Add 104 segmentation model to segment MRI cortical and sub-cortical structures. Each structure region is marked with a unique color/label compatible with FreeSurfer (5c0e388).
  • Add MRI tissue cropping pipeline to speedup the inference and lowering the memory use (8375a08).
  • Add new Buffer class supports 'uint8'|'int8'|'uint16'|'int16'| 'float16' to minimize memory overhead (7ce947b) and (5c0e388).
  • Fix memory leak (3f379ea).

Scientific Software - Peer-reviewed - JavaScript
Published by Mmasoud1 almost 4 years ago

Brainchop - brainchop-v1.1.0

#### Features:

  • Add mri_convert, a pre-processing converter to support reshaping/normalizing/resampling MRI raw input data (7b6ff1c)

Scientific Software - Peer-reviewed - JavaScript
Published by Mmasoud1 almost 4 years ago

Brainchop - brainchop-v1.0.0

We are excited to announce the first release of brainchop. This brings automatic 3D MRI segmentation capability to neuroimaging. You can use the online front-end brainchop.org or use it in the offline mode. Offline setup instructions are available on brainchop Wiki.

This package:

  • Supports inference on 3D volumetric MRI data with WebGL.
  • Supports full brain volume inference and subcube inference.
  • Supports post-processing and noise removal.
  • Supports saving resulting MRI labels in the Nifti format.
  • Supports pre-processing and normalization
  • Supports importing compatible pre-trained custom models in tfjs.

We welcome your feedback to help shape our priorities for brainchop. We also welcome contributors familiar with tfjs and neuroimaging applications who are interested in getting involved in expanding brainchop model zoo.

Looking forward to your contribution!

Scientific Software - Peer-reviewed - JavaScript
Published by Mmasoud1 about 4 years ago