From 3781a10e06a29e3a1a45d71470c8247898eb2af1 Mon Sep 17 00:00:00 2001 From: jo-mueller Date: Wed, 21 Aug 2024 09:16:00 +0000 Subject: [PATCH] deploy: c81fec767ae7cb066a27de011448a8756ceaabca --- .../johannes_mueller/yolo_from_omero/train_yolo.ipynb | 9 +++++++-- johannes_mueller/yolo_from_omero/train_yolo.html | 9 ++++++++- searchindex.js | 2 +- 3 files changed, 16 insertions(+), 4 deletions(-) diff --git a/_sources/johannes_mueller/yolo_from_omero/train_yolo.ipynb b/_sources/johannes_mueller/yolo_from_omero/train_yolo.ipynb index 6b58e61..5f6f5e6 100644 --- a/_sources/johannes_mueller/yolo_from_omero/train_yolo.ipynb +++ b/_sources/johannes_mueller/yolo_from_omero/train_yolo.ipynb @@ -253,6 +253,8 @@ "cell_type": "markdown", "metadata": {}, "source": [ + "### Train/Test/Validation split\n", + "\n", "Before we dive into the training, we have to do one final step. It is common practice in deep learning, to split the data into a training, validation and a testing cohort. This is done to evaluate the model on data it has not seen before. We will do a 70/20/10% split for training, validation and testing, respectively. We first create the folder structure:" ] }, @@ -642,7 +644,9 @@ "\n", "```{note}\n", " The steps up to this point can take a bit of time so you may have to reconnect to the omero server.\n", - "```" + "```\n", + "\n", + "One issue/question may arise here. *Where to upload the data?* My recommendation would be to create a new dataset on the omero server and upload the data there. In the following code, the dataset I created carries the id `260`, so'd have to replace this with the id of the dataset you created. *But why not just upload it tothe dataset I was already using up until here?* Well, you could do that, but it would be a bit messy because ad hoc it would be impossible to differentiate between the annotations you made manually above and the predictions done by YOLO. To keep it clean, it's better to create a new dataset." ] }, { @@ -654,7 +658,8 @@ "image_to_upload = io.imread(test_image)\n", "image_id = ezomero.post_image(\n", " conn, image=image_to_upload[None, None, None, :], dim_order='tczyx',\n", - " dataset_id=260, image_name='example_prediction'\n", + " dataset_id=260, # replace 260 with the id of the dataset you want to upload the image to\n", + " image_name='example_prediction'\n", " )\n", "\n", "roid_id = ezomero.post_roi(conn, image_id=image_id, shapes=rectangles)" diff --git a/johannes_mueller/yolo_from_omero/train_yolo.html b/johannes_mueller/yolo_from_omero/train_yolo.html index fc242d4..a20d188 100644 --- a/johannes_mueller/yolo_from_omero/train_yolo.html +++ b/johannes_mueller/yolo_from_omero/train_yolo.html @@ -410,6 +410,7 @@

Contents

  • Annotation
  • Training the model
  • Training