Alternatives and similar repositories for whole_brain_analysis:

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

• tpecot / WholeSlideImageAnalysisWithQuPath
  ☆25Updated 3 months ago
• labsyspharm / palom
  Piecewise alignment for layers of mosaics
  ☆24Updated last week
• ksugar / qupath-extension-cellsparse
  QuPath extension for Cellsparse
  ☆18Updated 4 months ago
• stegmaierj / Cellpose3D
  3D Extension of the Cellpose Algorithm by Stringer et al., 2021.
  ☆34Updated 2 years ago
• MouseLand / cellpose-napari
  napari plugin for cellpose (see www.cellpose.org) - an anatomical segmentation tool
  ☆52Updated 5 months ago
• AllenCell / aics-segmentation
  Part 1 of Allen Cell and Structure Segmenter: classic image segmentation workflow
  ☆28Updated 9 months ago
• AllenCell / aics-ml-segmentation
  ☆31Updated 2 years ago
• qupath / qupath-extension-align
  QuPath extension to interactively align images
  ☆23Updated 2 weeks ago
• qupath / qupath-extension-instanseg
  The official QuPath extension for InstanSeg
  ☆16Updated this week
• kreshuklab / go-nuclear
  Guides and code for 3D nuclear instance segmentation
  ☆22Updated last month
• haesleinhuepf / napari-accelerated-pixel-and-object-classification
  GPU-accelerated, OpenCL-based Random Forest Classifiers for pixel and labeled object classification in napari.
  ☆43Updated last year
• AllenCell / aics-shparam
  ☆20Updated last week
• saramcardle / FS2K
  Files associated with the From Samples To Knowledge 2025 QuPath training course
  ☆12Updated last week
• LabTrivedi / MOrgAna
  ☆28Updated 2 months ago
• clij / clupath
  GPU-accelerated image processing in QuPath
  ☆15Updated 3 years ago
• ahklemm / ImageJMacro_Introduction
  A first intoduction to scripting in Fiji using the ImageJ Macro language.
  ☆24Updated 6 months ago
• NHPatterson / napari-wsireg
  Whole slide image registration through wsireg in napari.
  ☆13Updated 2 years ago
• tpecot / DeepLearningBasedSegmentationForBiologists
  3-day workshop to teach biologists how to train and process deep convolutional neural networks for image segmentation through a comprehen…
  ☆12Updated 2 years ago
• ABIF-McGill / MethodsJ2
  MethodsJ2
  ☆14Updated 2 years ago
• TheJacksonLaboratory / dask_relabeling
  A relabeling tool for tiled segmentation with Dask
  ☆16Updated 7 months ago
• KerenLab / CellSighter
  ☆32Updated last year
• kreshuklab / MorphoFeatures
  MorphoFeatures code and data
  ☆20Updated last year
• RoccoDAnt / napari-zelda
  ZELDA: a 3D Image Segmentation and Parent to Child relation plugin for microscopy image analysis in napari
  ☆20Updated 4 months ago
• JaneliaSciComp / multifish
  EASI-FISH analysis pipeline for spatial transcriptomics
  ☆34Updated 5 months ago
• nygctech / PICASSO
  Development of PICASSO plugin for napari
  ☆16Updated 2 years ago
• MIAnalyzer / MIA
  Microsopic Image Analyzer (MIA)
  ☆29Updated last year
• jluethi / napari-feature-visualization
  Visualizing feature measurements on label images in napari
  ☆10Updated 9 months ago
• Kapoorlabs-CAPED / NapaTrackMater
  Napari Visualization tool for Trackmate > 6.0 and bTrackmate XML files for 2/3D + time tracks. Available via pip package napatrackmater.
  ☆16Updated 2 weeks ago
• haesleinhuepf / apoc
  Accelerated Pixel and Object Classifiers (APOC)
  ☆57Updated 2 months ago
• BioImaging-NKI / Cellpose-Fiji
  ImageJ macros to run Cellpose from Fiji (using the plugin from BIOP-EPFL) and to match nuclei and cell body label maps.
  ☆14Updated last month