Alternatives and similar repositories for codex

Users that are interested in codex are comparing it to the libraries listed below

• TuragaLab / flyvis
  A connectome-constrained deep mechanistic network (DMN) model of the fruit fly visual system in PyTorch.
  ☆99Updated 4 months ago
• brainglobe / brainglobe-atlasapi
  A Python interface to access neuroanatomical atlases
  ☆170Updated this week
• brainglobe / cellfinder
  Automated 3D cell detection in very large images
  ☆223Updated this week
• BIOP / ijp-imagetoatlas
  ABBA - Aligning Big Brains and Atlases (2D sections to 3D atlas registration)
  ☆56Updated last month
• brainglobe / brainreg
  Automated 3D brain registration with support for multiple species and atlases.
  ☆143Updated 3 weeks ago
• google-research / zapbench
  The Zebrafish Activity Prediction Benchmark measures progress on the problem of predicting cellular-resolution neural activity throughout…
  ☆62Updated 2 weeks ago
• brainglobe / brainglobe-segmentation
  Segmentation of anatomical structures in a common coordinate space
  ☆35Updated 3 weeks ago
• erturklab / delivr_cfos
  End-to-end light-sheet image analysis for mouse brains, with DL training data generated in VR
  ☆33Updated 3 weeks ago
• yu-lab-vt / AQuA
  An event-based tool for analyzing and quantifying calcium or neurotransmitter imaging data
  ☆55Updated last year
• nel-lab / FIOLA
  ☆34Updated 8 months ago
• kavli-ntnu / MINI2P_toolbox
  The codes, software, models, protocols, and etc. for building and using MINI2P to do the freely-moving recording and analysis. More detai…
  ☆104Updated 2 years ago
• albert597 / TRAILMAP
  ☆46Updated 5 years ago
• ChristophKirst / ClearMap
  ClearMap is a python toolbox for the analysis and registration of volumetric data from cleared tissues.
  ☆53Updated 5 years ago
• brainglobe / cellfinder-napari
  Efficient cell detection in large images using cellfinder in napari
  ☆22Updated 2 years ago
• JaneliaSciComp / VVDViewer
  3D/4D volumetric rendering of microscopy data
  ☆26Updated 2 months ago
• AllenInstitute / AllenSDK
  code for reading and processing Allen Institute for Brain Science data
  ☆374Updated 2 years ago
• voytekresearch / OscillatoryOrganoids
  Code for analyzing multi-electrode array recordings (spikes & LFP) for Trujillo, Gao, Negraes et al., 2019.
  ☆16Updated 5 years ago
• JaneliaSciComp / bigstream
  Tools for distributed alignment of massive images
  ☆92Updated 3 weeks ago
• e11bio / volara
  Block-wise operations for large nD volumes
  ☆43Updated 3 weeks ago
• tractatus / wholebrain
  R package for segmentation, registration and generating web-based brain atlases from microscope images
  ☆93Updated 4 years ago
• PolarBean / DeepSlice
  A python package which aligns histology to the Allen Brain Atlas and Waxholm rat atlas using deep learning.
  ☆112Updated 5 months ago
• brainglobe / brainreg-napari
  Automated 3D brain registration in napari with support for multiple species and atlases.
  ☆16Updated 2 years ago
• AdaptiveMotorControlLab / CellSeg3D
  A napari plugin for direct 3D cell segmentation -- taking you through training, inference, and review of masks
  ☆112Updated 3 months ago
• google-research / sofima
  Scalable Optical Flow-based Image Montaging and Alignment
  ☆87Updated last week
• navis-org / fafbseg-py
  Tools to work with the FlyWire connectome. Fully interoperable with navis.
  ☆19Updated this week
• danionella / warpfield
  GPU-based 3D non-rigid volumetric registration
  ☆43Updated 5 months ago
• AllenInstitute / patchseqtools
  QC and cell type assignment for patch-seq transcriptomics data
  ☆24Updated last year
• HelmchenLabSoftware / Cascade
  Calibrated inference of spiking from calcium ΔF/F data using deep networks
  ☆158Updated 2 weeks ago
• philshiu / Drosophila_brain_model
  A leaky integrate-and-fire computational model of the Drosophila brain
  ☆73Updated last year
• funkelab / daisy
  Block-wise task scheduling for large nD volumes.
  ☆33Updated 10 months ago