healthonrails

annolid

An annotation and instance segmentation-based multiple animal tracking and behavior analysis package.

cellmapping

Registering mouse brain images to an atlas and detecting and counting cells in different regions of the brain.

aicsimageio

Image Reading, Metadata Conversion, and Image Writing for Microscopy Images in Python

aind-ccf-registration

aind-smartspim-fuse

SmartSPIM module to generate OMEZarr data from fused images

aind-smartspim-quantification

Takes the output of segmentation and ccf registration to calculate cell counts per brain region

aind-smartspim-stitch

Stitching and fusion pipeline in the cloud

ANTsPy

Advanced Normalization Tools in Python

brainglobe-workflows

Workflows that utilise BrainGlobe tools to perform data analysis and visualisation.

BrainJ

Fiji pipeline for automated serial section reconstruction and mouse brain analysis.

Cutie

[arXiv 2023] Putting the Object Back Into Video Object Segmentation

DeepSlice

A python package which aligns histology to the Allen Brain Atlas and Waxholm rat atlas using deep learning.

dinov2

PyTorch code and models for the DINOv2 self-supervised learning method.

EdgeSAM

Official PyTorch implementation of "EdgeSAM: Prompt-In-the-Loop Distillation for On-Device Deployment of SAM"

EfficientSAM

EfficientSAM: Leveraged Masked Image Pretraining for Efficient Segment Anything

FollowAnything

healthonrails.github.io

LLaVA

Visual Instruction Tuning: Large Language-and-Vision Assistant built towards multimodal GPT-4 level capabilities.

MEDIAR

(NeurIPS 2022 CellSeg Challenge - 1st Winner) Open source code for "MEDIAR: Harmony of Data-Centric and Model-Centric for Multi-Modality Microscopy"

micro-sam

Segment Anything for Microscopy

nanosam

A distilled Segment Anything (SAM) model capable of running real-time with NVIDIA TensorRT

omnimotion

PoseAnything

segment-anything-fast

A batched offline inference oriented version of segment-anything

Segment-Everything-Everywhere-All-At-Once

Official implementation of the paper "Segment Everything Everywhere All at Once"

simba

SimBA (Simple Behavioral Analysis), a pipeline and GUI for developing supervised behavioral classifiers

TaskMatrix

tortoise-tts

A multi-voice TTS system trained with an emphasis on quality

TTS

🐸💬 - a deep learning toolkit for Text-to-Speech, battle-tested in research and production

yolov8_tracking

Real-time multi-object tracking and segmentation using YOLOv8