Owner
cytomining
17 indexed repositories · View on GitHub
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pycytominer
Python package for image-based profiling
Python · 145 stars
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DeepProfiler
Morphological profiling using deep learning
Python · 129 stars
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cytominer
Methods for Image-Based Cell Profiling
R · 52 stars
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copairs
Find profile pairs and compute retrieval metrics between them.
Python · 24 stars
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CytoTable
Harmonize high-content image analysis tool outputs for processing with Pycytominer and other Cytomining tools.
Python · 21 stars
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CytoDataFrame
An in-memory data analysis format for single-cell profiles alongside their corresponding images and segmentation masks.
Python · 13 stars
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profiling-recipe
Image-based Profiling Recipe
Python · 11 stars
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profiling-handbook
Image-based Profiling Handbook
11 stars
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coSMicQC
Single cell Morphology Quality Control (coSMicQC)
Python · 11 stars
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cytominer-database
[DEPRECATED] A package for storing morphological profiling data.
Python · 10 stars
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DeepProfiler-handbook
Documentation for installing and using of DeepProfiler
HTML · 8 stars
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cytominer-eval
[Deprecated] Common Evaluation Metrics for DataFrames
Python · 7 stars
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cytominer-vm
[DEPRECATED] Packer scripts to create VMs for running image-based profiling workflows on a cluster
Shell · 2 stars
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Dockerfile · 1 star
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pipeline-examples
Example pipelines for training purposes
Jupyter Notebook · 1 star
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.github
A special GitHub repository for setting the Cytomining organization profile and default community health files.
1 star
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profiling-template
Image-based Profiling Template
0 stars
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cytomining/cytominer-database#128 · 2 comments · 0 reactions · 0 assignees ·
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cytomining/cytominer-database#129 · 4 comments · 0 reactions · 0 assignees ·
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cytomining/cytominer-database#136 · 4 comments · 0 reactions · 0 assignees ·
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cytomining/pipeline-examples#4 · 9 comments · 0 reactions · 0 assignees ·
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enhancement
cytomining/profiling-recipe#8 · 0 comments · 0 reactions · 0 assignees ·
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enhancement
cytomining/profiling-recipe#11 · 2 comments · 0 reactions · 0 assignees ·
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enhancement
cytomining/profiling-recipe#12 · 1 comment · 0 reactions · 0 assignees ·
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enhancement good first issue
cytomining/profiling-recipe#13 · 0 comments · 0 reactions · 0 assignees ·
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enhancement
cytomining/profiling-recipe#14 · 0 comments · 0 reactions · 0 assignees ·
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enhancement
cytomining/profiling-recipe#29 · 0 comments · 0 reactions · 0 assignees ·
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Recipe wish list Openenhancement
cytomining/profiling-recipe#30 · 15 comments · 0 reactions · 0 assignees ·
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cytomining/profiling-recipe#34 · 0 comments · 0 reactions · 0 assignees ·
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cytomining/profiling-recipe#35 · 2 comments · 0 reactions · 0 assignees ·
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cytomining/profiling-recipe#38 · 0 comments · 0 reactions · 0 assignees ·
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Read .csv or .csv.gz Openenhancement
cytomining/profiling-recipe#41 · 0 comments · 0 reactions · 0 assignees ·
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bug
cytomining/profiling-recipe#43 · 0 comments · 0 reactions · 0 assignees ·
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cytomining/profiling-handbook#54 · 7 comments · 0 reactions · 0 assignees ·
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cytomining/profiling-handbook#70 · 8 comments · 0 reactions · 0 assignees ·
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cytomining/profiling-handbook#71 · 0 comments · 0 reactions · 0 assignees ·
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cytomining/profiling-handbook#74 · 1 comment · 0 reactions · 1 assignee ·
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cytomining/profiling-handbook#75 · 0 comments · 0 reactions · 0 assignees ·
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cytomining/profiling-template#6 · 1 comment · 0 reactions · 0 assignees ·
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documentation help wanted
cytomining/profiling-template#7 · 2 comments · 0 reactions · 1 assignee ·
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documentation enhancement
cytomining/profiling-template#8 · 0 comments · 0 reactions · 0 assignees ·
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enhancement
cytomining/profiling-template#9 · 0 comments · 0 reactions · 0 assignees ·
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enhancement
cytomining/profiling-template#10 · 0 comments · 0 reactions · 0 assignees ·
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enhancement
cytomining/profiling-template#11 · 0 comments · 0 reactions · 0 assignees ·
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cytomining/profiling-template#13 · 2 comments · 0 reactions · 0 assignees ·
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cytomining/profiling-template#15 · 3 comments · 0 reactions · 0 assignees ·
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cytomining/profiling-template#19 · 0 comments · 0 reactions · 0 assignees ·
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cytomining/profiling-template#20 · 0 comments · 0 reactions · 0 assignees ·
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cytomining/.github#5 · 0 comments · 0 reactions · 0 assignees ·
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enhancement
cytomining/copairs#20 · 0 comments · 0 reactions · 0 assignees ·
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bug
cytomining/copairs#45 · 0 comments · 0 reactions · 0 assignees ·
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bug
cytomining/copairs#52 · 0 comments · 0 reactions · 0 assignees ·
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enhancement
cytomining/copairs#66 · 0 comments · 1 reaction · 0 assignees ·
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documentation
cytomining/copairs#74 · 1 comment · 0 reactions · 0 assignees ·
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bug
cytomining/copairs#87 · 0 comments · 0 reactions · 0 assignees ·
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Remove Matcher class Openenhancement
cytomining/copairs#88 · 1 comment · 0 reactions · 0 assignees ·
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enhancement
cytomining/copairs#89 · 0 comments · 0 reactions · 0 assignees ·
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bug
cytomining/copairs#90 · 4 comments · 0 reactions · 0 assignees ·
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cytomining/copairs#93 · 2 comments · 0 reactions · 0 assignees ·
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cytomining/copairs#102 · 0 comments · 0 reactions · 0 assignees ·
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cytomining/copairs#105 · 0 comments · 0 reactions · 0 assignees ·
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cytomining/copairs#121 · 2 comments · 0 reactions · 0 assignees ·
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cytomining/copairs#129 · 0 comments · 0 reactions · 0 assignees ·
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enhancement
cytomining/DeepProfiler#25 · 0 comments · 0 reactions · 0 assignees ·
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enhancement
cytomining/DeepProfiler#136 · 1 comment · 0 reactions · 0 assignees ·
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enhancement
cytomining/DeepProfiler#239 · 0 comments · 0 reactions · 0 assignees ·
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help wanted question
cytomining/DeepProfiler#257 · 2 comments · 1 reaction · 0 assignees ·
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