other denoisplit data

dlmbl · Aug 23, 2024 · a771440 · a771440
1 parent 76eba37
commit a771440
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Showing 4 changed files with 18 additions and 14 deletions.
diff --git a/02_Noise2Void/solution.ipynb b/02_Noise2Void/solution.ipynb
@@ -231,7 +231,7 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "<div class=\"alert alert-block alert-success\"><h1><b>Checkpoint 1: What is N2V really doing?</b></h1>\n",
+    "<div class=\"alert alert-block alert-success\"><h1><b>Checkpoint 1: N2V masking</b></h1>\n",
     "</div>"
    ]
   },
@@ -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
@@ -396,7 +396,7 @@
    "source": [
     "<img src=\"resources/explainer.png\"/>\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
@@ -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
@@ -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