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