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smistad committed Mar 20, 2024
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11 changes: 7 additions & 4 deletions README.md
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<h1 align="center">FastPathology</h1>
<h3 align="center">Open-source software for deep learning-based digital pathology</h3>

[![GitHub Downloads](https://img.shields.io/github/downloads/SINTEFMedtek/FAST-Pathology/total?label=GitHub%20downloads&logo=github)](https://github.com/SINTEFMedtek/FAST-Pathology/releases)
[![License](https://img.shields.io/badge/License-BSD%202--Clause-orange.svg)](https://opensource.org/licenses/BSD-2-Clause)
![CI](https://github.com/AICAN-Research/FAST-Pathology/workflows/Build%20Windows/badge.svg?branch=master&event=push)
![CI](https://github.com/AICAN-Research/FAST-Pathology/workflows/Build%20Ubuntu/badge.svg?branch=master&event=push)
![CI](https://github.com/AICAN-Research/FAST-Pathology/workflows/Build%20macOS/badge.svg?branch=master&event=push)

**FastPathology** was created by SINTEF Medical Technology and the Norwegian University of Science and Technology (NTNU). A paper presenting the software and some benchmarks has been published in [IEEE Access](https://ieeexplore.ieee.org/document/9399433).
**FastPathology** was created by researchers at SINTEF and the Norwegian University of Science and Technology (NTNU). A paper presenting the software and some benchmarks has been published in [IEEE Access](https://ieeexplore.ieee.org/document/9399433).

<img src="data/Videos/fp_demo_v1.gif" style="background-color:black">
</div>
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</details>

## License

The source code of FastPathology is licensed under the BSD 2-clause license, however the FastPathology program use and are linked with many great third-party libraries which have several different open source licenses, see the licenses folder in the installation folder for more details.

## 📹 Demos and tutorials

Very simple demonstrations of the platform can be found on [Youtube](https://www.youtube.com/channel/UC4GM2KW54-vEZ0M1kH5-oig). More in-depth demonstrations will be added in the future. Wikis and tutorials can be found in the [wiki](https://github.com/SINTEFMedtek/FAST-Pathology/wiki). More information can be found from the **pages** section on the right in the wiki home.
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* **Use cases -** Patch-wise classification, low and high-resolution segmentation, and object detection are supported.
* **Inference Engines -** FAST includes a variety of different inference engines, i.e. TensorFlow CPU/CUDA (support both TF v1 and v2 models), TensorRT (UFF and ONNX), OpenVINO (CPU/GPU/VPU), and ONNX Runtime (CPU/GPU).
* **Text pipelines -** Possibility to create your own pipelines using the built-in script editor.
* **Formats -** Through OpenSlide FastPathology supports various WSI formats
* **Formats -** Through [OpenSlide](https://openslide.org/) FastPathology supports various WSI formats.

## 🔬 Applications of FastPathology

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- [Compile and install FAST on your system](https://fast.eriksmistad.no/building-fast.html).
2. Clone this repository
```bash
git clone https://github.com/SINTEFMedtek/FAST-Pathology.git
git clone https://github.com/AICAN-Research/FAST-Pathology.git
```
3. Setup build environment using CMake
*Linux (Ubuntu)*
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5 changes: 1 addition & 4 deletions source/gui/ProjectTab/ProjectWidget.cpp
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}

void ProjectWidget::selectFile() {
// TODO: Unable to read .zvi and .scn (Zeiss and Leica). I'm wondering if they are stored in some unexpected way (not image pyramids)
auto fileNames = QFileDialog::getOpenFileNames(this, tr("Select File(s)"), nullptr,
tr("WSI Files (*.tiff *.tif *.svs *.ndpi *.bif *.vms *.vsi *.mrxs *.otif);;All Files(*)"), //*.zvi *.scn)"),
nullptr, QFileDialog::DontUseNativeDialog);
auto fileNames = QFileDialog::getOpenFileNames(this, tr("Select File(s)"), nullptr,nullptr,nullptr, QFileDialog::DontUseNativeDialog);

auto progDialog = QProgressDialog(this);
progDialog.setRange(0, fileNames.count()-1);
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