System Requirements
System requirements for running GAT
GAT has been tested on Windows (10, 11) and on Mac OS.
Large images may lead to out-of-memory errors during analysis. The size of your image (pixels) and the pixel size (microns/pixel) affect the resizing required for accurate neuronal segmentation predictions. The necessary hardware specifications depend on the size of your image datasets.
The images are resized to a pixel size of 0.568 µm/px , so if your images have pixel sizes lower than this, images will be resized to a larger resolution -> making it bigger.
Hardware Requirements:
Any recent Intel/AMD CPU should work
RAM:
Minimum of 8GB
Recommended: 32 GB or more.
GPU: Not necessary, but it will make segmentation faster. Requires extra configuration.
Tests for neuronal segmentation
Summary of tests on sample images of different sizes for neuronal segmentation. Some of the example images are available here.
This was tested on a Windows 11 PC with 32 GB RAM without using a GPU.
Benchmarking was done using scripts from GAT -> Tools -> Test Neuron Probability.
Resolution: 1024 x 1024 pixels
Magnification: 40X
Pixel Size: 0.378 µm/px
Rescaled resolution used segmentation: 683 x 683 pixels
No. of tiles: 1
RAM used (MB): 200 - 300 MB RAM
Example dataset: ms_distal_colon_Hu_40X_1.tif
Within GAT, the no. of tiles is dynamically adjusted based on image size to prevent running out of memory.
Settings used for benchmarking are shown below. With the comparisons, the No. of tiles is the only setting that was altered which is documented above.
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