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5 results for “cellpose”
Cellpose model for Digital Phase Contrast images
<p><strong>Name: </strong>Cellpose model for Digital Phase Contrast images</p> <p><strong>Data type: </strong>Cellpose model, trained via transfer learning from ‘cyto’ model.</p> <p><strong>Training Dataset: </strong>Light microscopy (Digital Phase Contrast) and Manual annotations (<em>10.5281/zenodo.5996883</em>)</p> <p><strong>Training Procedure: </strong>Model was trained using a Cellpose version 0.6.5 with GPU support (NVIDIA GeForce RTX 2080) using default settings as per the <a href="https://cellpose.readthedocs.io/en/latest/train.html">Cellpose documentation</a> </p> <p>python -m cellpose --train --dir <em>TRAINING/DATASET/PATH/</em>train --test_dir <em>TRAINING/DATASET/PATH/</em>test --pretrained_model cyto --chan 0 --chan2 0</p> <p>The model file (MODEL NAME) in this repository is the result of this training.</p> <p><strong>Prediction Procedure: </strong>Using this model, a label image can be obtained from new unseen images in a given folder with</p> <p>python -m cellpose --dir <em>NEW/DATASET/PATH</em> --pretrained_model <em>FULL_MODEL_PATH</em> --chan 0 --chan2 0 --save_tif --no_npy</p>
Cellpose models for Label Prediction from Brightfield and Digital Phase Contrast images
<p><strong>Name: </strong>Cellpose models for Brightfield and Digital Phase Contrast images</p> <p><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).</p> <p><strong>Training Dataset: </strong>Light microscopy (Digital Phase Contrast or Brightfield) and automatic annotations (nuclei or cyto) (<a href="https://doi.org/10.5281/zenodo.6140064">https://doi.org/10.5281/zenodo.6140064</a>)</p> <p><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 <a href="https://cellpose.readthedocs.io/en/latest/train.html">Cellpose documentation</a> . Training was done using a <a href="https://datascience.ch/renku/">Renku </a>environment (<a href="https://github.com/BIOP/renku-templates/tree/main/VNC-Napari-Fiji-Omero-CUDA11.4-cellpose-omnipose">renku template</a>).</p> <p> </p> <p><strong>Command Line Execution for the different trained models</strong></p> <p><strong>nuclei_from_bf: </strong></p> <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> <p><strong>cyto_from_bf</strong>:</p> <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> <p> </p> <p><strong>nuclei_from_dpc:</strong></p> <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> <p><strong>cyto_from_dpc</strong>:</p> <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> <p> </p> <p><strong>nuclei_from_sqrdpc</strong>:</p> <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> <p><strong>cyto_from_sqrdpc</strong>:</p> <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> <p> </p> <p><em><strong>NOTE </strong></em>(§): We provide a notebook for Quality Control, which is an adaptation of the <a href="https://colab.research.google.com/github/HenriquesLab/ZeroCostDL4Mic/blob/master/Colab_notebooks/Beta%20notebooks/Cellpose_2D_ZeroCostDL4Mic.ipynb">"Cellpose (2D and 3D)" notebook from ZeroCostDL4Mic</a> .</p> <p><em><strong>NOTE</strong></em>: This dataset used a training dataset from the Zenodo entry(<a href="https://doi.org/10.5281/zenodo.6140064">https://doi.org/10.5281/zenodo.6140064</a>) generated from the “HeLa “Kyoto” cells under the scope” dataset Zenodo entry(<a href="https://doi.org/10.5281/zenodo.6139958">https://doi.org/10.5281/zenodo.6139958</a>) in order to automatically generate the label images.</p> <p><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.</p> <p> </p>
Cellpose training data and scripts from "Machine learning for histological annotation and quantification of cortical layers"
<p>This Workflow contains all the material necessary to reproduce the cells detection, thanks to the QuPath performed in the paper</p> <p> "<strong>Machine learning for histological annotation and quantification of cortical layers</strong>"</p> <p>Inside this workflow and dataset, you will find the following folders</p> <ol> <li><strong>QuPath Training Project</strong>: A QuPath 0.5.0 project containing all the manual annotations (ground truths) used to train the cellpose model, as well as the script to start the training</li> <li><strong>Training Images</strong> and <strong>Demo Images</strong>: The raw whole slide scanner images needed by the above QuPath project</li> <li><strong>Model</strong>: The fodler containing the trained cellpose model</li> <li><strong>cellpose-training Folder</strong>: The exported raw and ground truth images that the above cellpose model was trained on</li> <li><strong>Scripts</strong>: The QuPath scripts, also located in their respective QuPath projects, that were created for this whole workflow</li> <li><strong>QC</strong>: A Jupyter notebook, based on ZeroCostDL4Mic that computes quality metrics in order to assess the performance of the trained cellpose model. The folder also contains the resulting metrics.</li> </ol> <p>Installation and Use</p> <p>If you are going to use the QuPath projects, you need a local QuPath Installation https://qupath.github.io/ that is configured to run the QuPath Cellpose Extension https://github.com/BIOP/qupath-extension-cellpose as well as a working Cellpose installation https://github.com/MouseLand/cellpose</p> <p>Instructions for installation are available from the links above.</p> <p>After that, you should be able to open the QuPath project, navigate to the "Automate > Project scripts" menu and locate the script you wish to run.</p> <p><br>1. train a cell segmentation algorithm in the context of the rat brain Layer <br>Boundaries project </p> <p>2. trigger cell segmentation from a QuPath project in a semi-automated pipeline</p>
Tracking Glioblastoma-astrocytoma cells imaged in brightfield with TrackMate-Cellpose
<p>Glioblastoma-astrocytoma U373 cells migrating on a polyacrylamide gel.</p> <p>This dataset is used in a tutorial on using TrackMate and its cellpose integration to track such cells in brightfield, using a custom cellpose model (included in the dataset).</p> <p>See here for details: <a href="https://imagej.net/plugins/trackmate/trackmate-cellpose">https://imagej.net/plugins/trackmate/trackmate-cellpose</a> </p>
Tracking breast cancer cells migrating collectively and imaged in fluorescence with TrackMate-Cellpose
<p>Breast cancer cells migrating collectively.</p> <p>This dataset is used in a tutorial on using TrackMate and its cellpose integration to track such cells.</p> <p>See here for details: <a href="https://imagej.net/plugins/trackmate/trackmate-cellpose">https://imagej.net/plugins/trackmate/trackmate-cellpose</a> </p>
ScienceDex guides
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These curated guides explain access requirements, typical timelines, costs, and reuse considerations for widely used research datasets.
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