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Title: GitHub - HelmchenLabSoftware/Cascade: Calibrated inference of spiking from calcium ΔF/F data using deep networks

Open Graph Title: GitHub - HelmchenLabSoftware/Cascade: Calibrated inference of spiking from calcium ΔF/F data using deep networks

X Title: GitHub - HelmchenLabSoftware/Cascade: Calibrated inference of spiking from calcium ΔF/F data using deep networks

Description: Calibrated inference of spiking from calcium ΔF/F data using deep networks - HelmchenLabSoftware/Cascade

Open Graph Description: Calibrated inference of spiking from calcium ΔF/F data using deep networks - HelmchenLabSoftware/Cascade

X Description: Calibrated inference of spiking from calcium ΔF/F data using deep networks - HelmchenLabSoftware/Cascade

Mail addresses
p.t.r.rupprecht+cascade@gmail.com
p.t.r.rupprecht+cascade@gmail.com
p.t.r.rupprecht+cascade@gmail.com

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Ground_truth	https://patch-diff.githubusercontent.com/HelmchenLabSoftware/Cascade/tree/master/Ground_truth
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cascade2p	https://patch-diff.githubusercontent.com/HelmchenLabSoftware/Cascade/tree/master/cascade2p
cascade2p	https://patch-diff.githubusercontent.com/HelmchenLabSoftware/Cascade/tree/master/cascade2p
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README.md	https://patch-diff.githubusercontent.com/HelmchenLabSoftware/Cascade/blob/master/README.md
setup.py	https://patch-diff.githubusercontent.com/HelmchenLabSoftware/Cascade/blob/master/setup.py
setup.py	https://patch-diff.githubusercontent.com/HelmchenLabSoftware/Cascade/blob/master/setup.py
README	https://patch-diff.githubusercontent.com/HelmchenLabSoftware/Cascade
GPL-3.0 license	https://patch-diff.githubusercontent.com/HelmchenLabSoftware/Cascade
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	https://github.com/HelmchenLabSoftware/Cascade/blob/master/LICENSE
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	https://github.com/HelmchenLabSoftware/Calibrated-inference-of-spiking/blob/master/etc/CA1_deconvolution_CASCADE.gif
the main paper	https://www.nature.com/articles/s41593-021-00895-5
spinal cord data	https://www.biorxiv.org/content/10.1101/2024.07.17.603957
GCaMP8	https://www.biorxiv.org/content/10.1101/2025.03.03.641129
Spike inference from calcium data	https://colab.research.google.com/github/HelmchenLabSoftware/Cascade/blob/master/Demo%20scripts/Calibrated_spike_inference_with_Cascade.ipynb
	https://patch-diff.githubusercontent.com/HelmchenLabSoftware/Cascade#spike-inference-from-calcium-data
Spike inference from calcium data	https://colab.research.google.com/github/HelmchenLabSoftware/Cascade/blob/master/Demo%20scripts/Calibrated_spike_inference_with_Cascade.ipynb
	https://colab.research.google.com/github/HelmchenLabSoftware/Cascade/blob/master/Demo%20scripts/Calibrated_spike_inference_with_Cascade.ipynb
	https://patch-diff.githubusercontent.com/HelmchenLabSoftware/Cascade#updates-to-ground-truth-datasets-and-pretrained-models
CascadeTorch	https://github.com/PTRRupprecht/CascadeTorch
please reach out	https://github.com/HelmchenLabSoftware/Cascade/issues/81
#76	https://github.com/HelmchenLabSoftware/Cascade/issues/76
openly accessible manuscript	https://doi.org/10.1523/JNEUROSCI.1187-24.2025
blog post	https://gcamp6f.com/2025/04/25/accuaretly-computing-noise-levels-for-calcium-imaging-data/
preprint	https://www.biorxiv.org/content/10.1101/2025.03.03.641129v1
FAQ section	https://github.com/HelmchenLabSoftware/Cascade?tab=readme-ov-file#can-i-apply-cascade-to-data-recorded-with-interneurons
preprint	https://www.biorxiv.org/content/10.1101/2025.03.03.641129v1
blog post	https://gcamp6f.com/2025/03/24/online-spike-inference-with-gcamp8/
blog post	https://gcamp6f.com/2025/03/21/detecting-single-spikes-from-calcium-imaging/
blog post	https://gcamp6f.com/2025/03/14/non-linearity-of-calcium-indicators-history-dependence-of-spike-reporting/
New preprint	https://www.biorxiv.org/content/10.1101/2025.03.03.641129
preprint	https://www.biorxiv.org/content/10.1101/2024.07.17.603957v1
blog post	https://gcamp6f.com/2024/08/22/spike-inference-with-gcamp8-new-pretrained-models-available/
A new preprint	https://www.biorxiv.org/content/10.1101/2024.07.17.603957v1
#43	https://github.com/HelmchenLabSoftware/Cascade/issues/43
#28	https://github.com/HelmchenLabSoftware/Cascade/issues/28
Exploration of the ground truth database	https://colab.research.google.com/github/HelmchenLabSoftware/Cascade/blob/master/Demo%20scripts/Explore_ground_truth_datasets.ipynb
	https://patch-diff.githubusercontent.com/HelmchenLabSoftware/Cascade#exploration-of-the-ground-truth-database
Exploration of the ground truth database	https://colab.research.google.com/github/HelmchenLabSoftware/Cascade/blob/master/Demo%20scripts/Explore_ground_truth_datasets.ipynb
	https://colab.research.google.com/github/HelmchenLabSoftware/Cascade/blob/master/Demo%20scripts/Explore_ground_truth_datasets.ipynb
	https://patch-diff.githubusercontent.com/HelmchenLabSoftware/Cascade#getting-started
	https://patch-diff.githubusercontent.com/HelmchenLabSoftware/Cascade#without-installation
this online Colaboratory Notebook	https://colab.research.google.com/github/HelmchenLabSoftware/Cascade/blob/master/Demo%20scripts/Calibrated_spike_inference_with_Cascade.ipynb
	https://patch-diff.githubusercontent.com/HelmchenLabSoftware/Cascade#with-a-local-installation-ubuntuwindows
https://www.anaconda.com/distribution/	https://www.anaconda.com/distribution/
here	https://stackoverflow.com/questions/58068818/how-to-use-jupyter-notebooks-in-a-conda-environment
DeepLabCut	https://github.com/DeepLabCut/DeepLabCut/blob/master/docs/installation.md
	https://patch-diff.githubusercontent.com/HelmchenLabSoftware/Cascade#with-a-local-installation-macos
Matúš Halák	https://github.com/matushalak
check it out!	https://github.com/HelmchenLabSoftware/Cascade/issues/46#issuecomment-2765456770
related issue	https://github.com/HelmchenLabSoftware/Cascade/issues/46
Link to instructions	https://github.com/HelmchenLabSoftware/Cascade/blob/master/etc/Instructions_Mac2024.md
https://stackoverflow.com/questions/53014306/error-15-initializing-libiomp5-dylib-but-found-libiomp5-dylib-already-initial	https://stackoverflow.com/questions/53014306/error-15-initializing-libiomp5-dylib-but-found-libiomp5-dylib-already-initial
	https://patch-diff.githubusercontent.com/HelmchenLabSoftware/Cascade#typical-work-flow
Colaboratory Notebook	https://colab.research.google.com/github/HelmchenLabSoftware/Cascade/blob/master/Demo%20scripts/Calibrated_spike_inference_with_Cascade.ipynb
link	https://www.nature.com/articles/s41593-021-00895-5
work on GCaMP8	https://www.biorxiv.org/content/10.1101/2025.03.03.641129v3
paper	https://www.nature.com/articles/s41593-021-00895-5
	https://patch-diff.githubusercontent.com/HelmchenLabSoftware/Cascade#under-the-hood
paper	https://www.nature.com/articles/s41593-021-00895-5
paper	https://www.nature.com/articles/s41593-021-00895-5
	https://patch-diff.githubusercontent.com/HelmchenLabSoftware/Cascade#frequently-asked-questions
	https://patch-diff.githubusercontent.com/HelmchenLabSoftware/Cascade#what-does-the-output-of-the-algorithm-mean
	https://patch-diff.githubusercontent.com/HelmchenLabSoftware/Cascade#can-spike_prob-be-larger-than-1
	https://patch-diff.githubusercontent.com/HelmchenLabSoftware/Cascade#how-large-would-a-single-spike-be
	https://patch-diff.githubusercontent.com/HelmchenLabSoftware/Cascade#how-precise-and-good-are-my-predictions
the demo script	https://github.com/HelmchenLabSoftware/Cascade/blob/master/Demo%20scripts/Demo_benchmark_model.py
paper	https://www.nature.com/articles/s41593-021-00895-5
	https://patch-diff.githubusercontent.com/HelmchenLabSoftware/Cascade#can-i-apply-cascade-to-data-recorded-with-gcamp8
GCaMP8 paper	https://www.nature.com/articles/s41586-023-05828-9
	https://patch-diff.githubusercontent.com/HelmchenLabSoftware/Cascade#can-i-apply-cascade-to-data-recorded-with-interneurons
Zhang et al. (2023)	https://www.nature.com/articles/s41586-023-05828-9
Rupprecht et al. (2025)	https://www.biorxiv.org/content/10.1101/2025.03.03.641129
Hal Rockwell	https://github.com/hal-rock
	https://patch-diff.githubusercontent.com/HelmchenLabSoftware/Cascade#why-is-the-output-of-the-algorithm-a-probability-why-not-discrete-spikes
paper	https://www.nature.com/articles/s41593-021-00895-5
demo	https://github.com/HelmchenLabSoftware/Cascade/blob/master/Demo%20scripts/Demo_discrete_spikes.py
	https://patch-diff.githubusercontent.com/HelmchenLabSoftware/Cascade#why-are-the-first-and-last-datapoints-of-the-predictions-nans
	https://patch-diff.githubusercontent.com/HelmchenLabSoftware/Cascade#should-i-smooth-the-dff-traces-before-i-feed-them-into-cascade
issue #53	https://github.com/HelmchenLabSoftware/Cascade/issues/53
	https://patch-diff.githubusercontent.com/HelmchenLabSoftware/Cascade#i-get-a-certain-noise-level-for-my-recordings-what-is-good-or-bad
paper	https://www.nature.com/articles/s41593-021-00895-5
paper	https://www.nature.com/articles/s41593-021-00895-5
	https://patch-diff.githubusercontent.com/HelmchenLabSoftware/Cascade#how-do-i-select-an-appropriate-model-for-my-data
paper	https://www.nature.com/articles/s41593-021-00895-5
	https://patch-diff.githubusercontent.com/HelmchenLabSoftware/Cascade#what-does-the-global-exc-for-some-of-the-models-mean
paper	https://www.nature.com/articles/s41593-021-00895-5
	https://patch-diff.githubusercontent.com/HelmchenLabSoftware/Cascade#what-does-the-smoothing-parameter-for-the-models-mean
paper	https://www.nature.com/articles/s41593-021-00895-5
	https://patch-diff.githubusercontent.com/HelmchenLabSoftware/Cascade#what-does-the-causal-mean-for-some-of-the-models
paper	https://www.nature.com/articles/s41593-021-00895-5
	https://patch-diff.githubusercontent.com/HelmchenLabSoftware/Cascade#how-can-i-use-cascade-for-online-spike-inference
Github	https://github.com/HelmchenLabSoftware/Cascade
preprint	https://www.biorxiv.org/content/10.1101/2025.03.03.641129v1
blog post	https://gcamp6f.com/2025/03/24/online-spike-inference-with-gcamp8/
	https://patch-diff.githubusercontent.com/HelmchenLabSoftware/Cascade#none-of-the-models-is-good-for-me-what-can-i-do
Github page	https://github.com/HelmchenLabSoftware/Cascade
	https://patch-diff.githubusercontent.com/HelmchenLabSoftware/Cascade#how-can-i-inspect-the-ground-truth-datasets
As described above	https://github.com/HelmchenLabSoftware/Cascade?tab=readme-ov-file#exploration-of-the-ground-truth-database
here	https://github.com/HelmchenLabSoftware/Cascade/blob/607358103389fac7a851ec0b74342ffc01fc7abc/cascade2p/utils.py#L686
here	https://github.com/HelmchenLabSoftware/Cascade/blob/607358103389fac7a851ec0b74342ffc01fc7abc/cascade2p/utils.py#L686
	https://patch-diff.githubusercontent.com/HelmchenLabSoftware/Cascade#i-have-my-own-ground-truth-dataset-how-can-i-use-it
ground truth	https://github.com/HelmchenLabSoftware/Cascade/tree/master/Ground_truth
	https://patch-diff.githubusercontent.com/HelmchenLabSoftware/Cascade#i-want-to-use-my-own-ground-truth-dataset-but-i-dont-want-to-share-it
CaImAn	https://github.com/flatironinstitute/CaImAn
	https://patch-diff.githubusercontent.com/HelmchenLabSoftware/Cascade#can-i-use-the-algorithm-also-locally-eg-within-caiman-or-in-my-own-pipeline
Github repository	https://github.com/HelmchenLabSoftware/Cascade
	https://patch-diff.githubusercontent.com/HelmchenLabSoftware/Cascade#can-i-use-cascade-as-well-for-endoscopic-1p-calcium-imaging-data
CNMF-E	https://elifesciences.org/articles/28728
	https://patch-diff.githubusercontent.com/HelmchenLabSoftware/Cascade#i-would-like-to-look-at-the-ground-truth-data
Github repository	https://github.com/HelmchenLabSoftware/Cascade
Colaboratory Notebook	https://colab.research.google.com/github/HelmchenLabSoftware/Cascade/blob/master/Demo%20scripts/Explore_ground_truth_datasets.ipynb
	https://patch-diff.githubusercontent.com/HelmchenLabSoftware/Cascade#which-reference-should-i-cite
paper	https://www.nature.com/articles/s41593-021-00895-5
Spike inference from calcium imaging data acquired with GCaMP8 indicators	https://www.biorxiv.org/content/10.1101/2025.03.03.641129
Spike rate inference from mouse spinal cord calcium imaging data	https://www.jneurosci.org/content/45/18/e1187242025
deep-learning	https://patch-diff.githubusercontent.com/topics/deep-learning
calcium-imaging	https://patch-diff.githubusercontent.com/topics/calcium-imaging
deconvolution	https://patch-diff.githubusercontent.com/topics/deconvolution
spike-detection	https://patch-diff.githubusercontent.com/topics/spike-detection
two-photon	https://patch-diff.githubusercontent.com/topics/two-photon
Readme	https://patch-diff.githubusercontent.com/HelmchenLabSoftware/Cascade#readme-ov-file
GPL-3.0 license	https://patch-diff.githubusercontent.com/HelmchenLabSoftware/Cascade#GPL-3.0-1-ov-file
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158 stars	https://patch-diff.githubusercontent.com/HelmchenLabSoftware/Cascade/stargazers
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51 forks	https://patch-diff.githubusercontent.com/HelmchenLabSoftware/Cascade/forks
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Releases 2	https://patch-diff.githubusercontent.com/HelmchenLabSoftware/Cascade/releases
Cascade 2.0 Latest Mar 11, 2025	https://patch-diff.githubusercontent.com/HelmchenLabSoftware/Cascade/releases/tag/v2.0
+ 1 release	https://patch-diff.githubusercontent.com/HelmchenLabSoftware/Cascade/releases
Packages 0	https://patch-diff.githubusercontent.com/orgs/HelmchenLabSoftware/packages?repo_name=Cascade
Please reload this page	https://patch-diff.githubusercontent.com/HelmchenLabSoftware/Cascade
Contributors 8	https://patch-diff.githubusercontent.com/HelmchenLabSoftware/Cascade/graphs/contributors
Please reload this page	https://patch-diff.githubusercontent.com/HelmchenLabSoftware/Cascade
Jupyter Notebook 90.9%	https://patch-diff.githubusercontent.com/HelmchenLabSoftware/Cascade/search?l=jupyter-notebook
Python 9.0%	https://patch-diff.githubusercontent.com/HelmchenLabSoftware/Cascade/search?l=python
Dockerfile 0.1%	https://patch-diff.githubusercontent.com/HelmchenLabSoftware/Cascade/search?l=dockerfile
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