Repositories list

• DeepTile

  Public
  Large image tiling and stitching library for scaling Python functions to arbitrary input image sizes.

  Python

  •

  MIT License

  •0•13•1•0•Updated Jan 17, 2025Jan 17, 2025

• ImageAnalysisProject

  Public
  Python

  •1•0•0•0•Updated Jan 16, 2025Jan 16, 2025

• NimbusImage

  Public
  UPenn ?

  Vue

  •

  Apache License 2.0

  •6•8•128•10•Updated Jan 13, 2025Jan 13, 2025

• l-metric

  Public
  Jupyter Notebook

  •

  Apache License 2.0

  •0•0•0•0•Updated Jan 10, 2025Jan 10, 2025

• tools-for-science

  Public
  Apache License 2.0

  •0•1•0•0•Updated Oct 30, 2024Oct 30, 2024

• process_incucyte_tiff_data

  Public
  Python

  •

  Apache License 2.0

  •0•0•3•0•Updated Oct 12, 2024Oct 12, 2024

• SGanalysis

  Public
  Analysis for Spatial Genomics GenePS data

  Python

  •

  Apache License 2.0

  •1•1•0•0•Updated Oct 7, 2024Oct 7, 2024

• segment-anything-2-nimbus

  Public
  The repository provides code for running inference with the Meta Segment Anything Model 2 (SAM 2), links for downloading the trained model checkpoints, and example notebooks that show how to use the model.

  Jupyter Notebook

  •

  Apache License 2.0

  •1.4k•0•0•0•Updated Oct 6, 2024Oct 6, 2024

• NimbusImageChatbot

  Public
  Vue

  •

  Apache License 2.0

  •0•0•0•0•Updated Aug 25, 2024Aug 25, 2024

• ProbeDesign

  Public
  MATLAB

  •3•4•1•2•Updated Aug 21, 2024Aug 21, 2024

• nimbus_sandboxes

  Public
  Jupyter Notebook

  •

  GNU General Public License v3.0

  •0•0•0•0•Updated Jul 3, 2024Jul 3, 2024

• iPSC_Rewind

  Public
  R

  •

  MIT License

  •0•0•0•0•Updated Jan 8, 2024Jan 8, 2024

• combine-ome-tiff

  Public
  Combines files spread across multiple OME TIFFs into a single TIFF

  Python

  •

  Apache License 2.0

  •0•0•0•0•Updated Dec 13, 2023Dec 13, 2023

• NimbusImageGitBook

  Public
  Apache License 2.0

  •0•0•0•0•Updated Sep 23, 2023Sep 23, 2023

• nimbusimage-documentation

  Public template
  NimbusImage documentation

  Python

  •1.5k•0•0•0•Updated Aug 16, 2023Aug 16, 2023

• timemachine

  Public
  initial commit of timemachine sequence analysis repository

  Python

  •1•0•0•0•Updated Aug 8, 2023Aug 8, 2023

• FateMap_Goyal2023

  Public
  MATLAB

  •

  MIT License

  •0•0•1•0•Updated Jun 3, 2023Jun 3, 2023

• ClonoCluster_paper

  Public
  Raw data and analysis scripts for the BarCluster paper

  R

  •

  GNU General Public License v3.0

  •0•0•0•0•Updated Dec 3, 2022Dec 3, 2022

• lost-in-space-public

  Public
  public repository to recreate analyses in allelic correlation + noise transmission paper

  MATLAB

  •0•0•0•0•Updated Sep 16, 2022Sep 16, 2022

• organoids2

  Public
  MATLAB

  •0•1•0•0•Updated Mar 23, 2022Mar 23, 2022

• rajlabimagetools

  Public
  MATLAB

  •4•2•2•0•Updated Mar 23, 2022Mar 23, 2022

• cardiacdiff_fatemap

  Public
  R

  •

  MIT License

  •0•0•0•0•Updated Feb 11, 2022Feb 11, 2022

• scratchassay

  Public
  MATLAB

  •0•0•0•0•Updated Dec 22, 2021Dec 22, 2021

• Cellcount_Seahorse_Microplate

  Public
  MATLAB

  •0•0•0•0•Updated Dec 21, 2021Dec 21, 2021

• blobCounter

  Public
  0•0•0•0•Updated Dec 21, 2021Dec 21, 2021

• dentist2

  Public
  MATLAB

  •1•0•0•0•Updated Dec 14, 2021Dec 14, 2021

• P3_public_analysis

  Public
  R

  •

  MIT License

  •0•0•0•0•Updated Jul 4, 2021Jul 4, 2021

• Trident

  Public
  Jupyter Notebook

  •0•0•0•0•Updated Jun 4, 2021Jun 4, 2021

• rajlabformattools

  Public
  MATLAB

  •1•0•0•0•Updated May 4, 2021May 4, 2021

• atac-seq_pipeline_paired-end

  Public
  Slightly customized version of the ENCODE ATAC-seq v1 pipeline. Made to run on Penn's high performance cluster (PMACS). The ENCODE ATAC-Seq pipeline v1 specifications are listed in this google doc: (specs at https://docs.google.com/document/d/1f0Cm4vRyDQDu0bMehHD7P7KOMxTOP-HiNoIvL1VcBt8/edit#heading=h.9ecc41kilcvq

  Python

  •

  MIT License

  •0•1•0•0•Updated Feb 25, 2021Feb 25, 2021