Cellpose models for Label Prediction from Brightfield and Digital Phase Contrast images

<strong>Name: </strong>Cellpose models for Brightfield and Digital Phase Contrast images <strong>Data type: </strong>Cellpose models trained via transfer learning from the ‘nuclei’ and ‘cyto2’ pretrained model with additional <strong>Training Dataset . Includes</strong> corresponding csv files with 'Quality Control' metrics(§) (model.zip). <strong>Training Dataset: </strong>Light microscopy (Digital Phase Contrast or Brightfield) and automatic annotations (nuclei or cyto) (https://doi.org/10.5281/zenodo.6140064) <strong>Training Procedure: </strong>The cellpose models were trained using cellpose version 1.0.0 with GPU support (NVIDIA GeForce K40) using default settings as per the Cellpose documentation . Training was done using a Renku environment (renku template). <strong>Command Line Execution for the different trained models</strong> <strong>nuclei_from_bf: </strong> <pre><code class="language-python">cellpose --train --dir 'data/train/' --test_dir 'data/test/' --pretrained_model nuclei --img_filter _bf --mask_filter _nuclei --chan 0 --chan2 0 --use_gpu --verbose</code></pre> <strong>cyto_from_bf</strong>: <pre><code class="language-python">cellpose --train --dir 'data/train/' --test_dir 'data/test/' --pretrained_model cyto2 --img_filter _bf --mask_filter _cyto --chan 0 --chan2 0 --use_gpu --verbose</code></pre> <strong>nuclei_from_dpc:</strong> <pre><code class="language-python">cellpose --train --dir 'data/train/' --test_dir 'data/test/' --pretrained_model nuclei --img_filter _dpc --mask_filter _nuclei --chan 0 --chan2 0 --use_gpu --verbose</code></pre> <strong>cyto_from_dpc</strong>: <pre><code>cellpose --train --dir 'data/train/' --test_dir 'data/test/' --pretrained_model cyto2 --img_filter _dpc --mask_filter _cyto --chan 0 --chan2 0 --use_gpu --verbose</code></pre> <strong>nuclei_from_sqrdpc</strong>: <pre><code class="language-python">cellpose --train --dir 'data/train/' --test_dir 'data/test/' --pretrained_model nuclei --img_filter _sqrdpc --mask_filter _nuclei --chan 0 --chan2 0 --use_gpu --verbose</code></pre> <strong>cyto_from_sqrdpc</strong>: <pre><code class="language-python">cellpose --train --dir 'data/train/' --test_dir 'data/test/' --pretrained_model cyto2 --img_filter _sqrdpc --mask_filter _cyto --chan 0 --chan2 0 --use_gpu --verbose</code></pre> <em><strong>NOTE </strong></em>(§): We provide a notebook for Quality Control, which is an adaptation of the "Cellpose (2D and 3D)" notebook from ZeroCostDL4Mic . <em><strong>NOTE</strong></em>: This dataset used a training dataset from the Zenodo entry(https://doi.org/10.5281/zenodo.6140064) generated from the “HeLa “Kyoto” cells under the scope” dataset Zenodo entry(https://doi.org/10.5281/zenodo.6139958) in order to automatically generate the label images. <strong><em>NOTE</em></strong>:<strong> </strong>Make sure that you delete the “_flow” images that are auto-computed when running the training. If you do not, then the flows from previous runs will be used for the new training, which might yield confusing results.