diff --git a/02_Noise2Void/solution.ipynb b/02_Noise2Void/solution.ipynb index 990a397..6a92097 100755 --- a/02_Noise2Void/solution.ipynb +++ b/02_Noise2Void/solution.ipynb @@ -231,7 +231,7 @@ "cell_type": "markdown", "metadata": {}, "source": [ - "

Checkpoint 1: What is N2V really doing?

\n", + "

Checkpoint 1: N2V masking

\n", "
" ] }, @@ -389,16 +389,6 @@ "careamist = CAREamist(source=training_config)" ] }, - { - "cell_type": "code", - "execution_count": null, - "metadata": {}, - "outputs": [], - "source": [ - "%load_ext tensorboard\n", - "%tensorboard --logdir logs/lightning_logs" - ] - }, { "attachments": {}, "cell_type": "markdown", diff --git a/03_COSDD/solution.ipynb b/03_COSDD/solution.ipynb index 7656e6d..7aae351 100755 --- a/03_COSDD/solution.ipynb +++ b/03_COSDD/solution.ipynb @@ -396,7 +396,7 @@ "source": [ "\n", "\n", - "COSDD is a Variational Autoencoder~\\cite{chenvariational} (solid arrows) trained to model the distribution of noisy images $\\mathbf{x}$. \n", + "COSDD is a Variational Autoencoder (solid arrows) trained to model the distribution of noisy images $\\mathbf{x}$. \n", "The autoregressive (AR) decoder models the noise component of the images, while the latent variable models only the clean signal component $\\mathbf{s}$.\n", "In a second step (dashed arrows), the \\emph{signal decoder} is trained to map latent variables into image space, producing an estimate of the signal underlying $\\mathbf{x}$.\n", "{\\bf b):}\n", @@ -757,7 +757,7 @@ "outputs": [], "source": [ "lowsnr_path = \"./../data/mito-confocal-lowsnr.tif\"\n", - "n_test_images = 10\n", + "n_test_images = 5\n", "# load the data\n", "test_set = tifffile.imread(lowsnr_path)\n", "test_set = test_set[:n_test_images, np.newaxis]\n", diff --git a/README.md b/README.md index e8a95b7..c1ffa20 100755 --- a/README.md +++ b/README.md @@ -23,7 +23,7 @@ source setup.sh 1. [Context-aware restoration](01_CARE/care_exercise.ipynb) 2. [Noise2Void](02_Noise2Void/n2v_exercise.ipynb) -3. [COSDD](03_COSDD/exercise.ipynb) +3. [Correlated and Signal Dependent Denoising (COSDD)](03_COSDD/exercise.ipynb) 4. [DenoiSplit](04_DenoiSplit/exercise.ipynb) diff --git a/setup.sh b/setup.sh index 04a6ab6..82df4f5 100755 --- a/setup.sh +++ b/setup.sh @@ -36,6 +36,20 @@ if [[ "$CONDA_DEFAULT_ENV" == "$ENV" ]]; then mkdir ER/ cd ER/ gdown 1Bho6Oymfxi7OV0tPb9wkINkVOCpTaL7M + cd ../ + mkdir Microtubules/ + cd Microtubules/ + gdown 14sPIEE2qU2J6oRFMz46v2IvkCVjFX8D1 + cd ../ + mkdir F-actin/ + cd F-actin/ + gdown 1FYO-Bpl5vjpiJ6kzV1qO1pL37Y3Dirfy + gdown 1DWcezoHxPClA1SDYdXKIHooiDiRldEyq + cd ../ + mkdir F-actin_Nonlinear/ + cd F-actin_Nonlinear/ + gdown 1xwZH_XNbwXmq1HZGYXnePdRWP2yavgKg + gdown 1L_dpsEGWmMd4hEXbbmY8X2Gc-MMWUKLN cd ../../ mkdir 03_COSDD/checkpoints cd 03_COSDD/checkpoints