First instance segmentation training and prediction with lightning flash

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view raw smallsample_125_displaycoco_train-predict_with_lightning-flash.ipynb hosted with ❤ by GitHub

Making an annotated Dataset:

125 grey-scaled images of overlapping pairs of chromosomes were annotated with makesense.ai. Annotation was saved in a single json file in COCO format:

Each image has two instances of a single "chromosome" label.

Loading and training a maskrcnn model

Lightning-flash was used to load and train a mask-rcnn model over the dataset:

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view raw smallsample_125_displaycoco_train-predict_with_lightning-flash.ipynb hosted with ❤ by GitHub

Possible issue with the dataset.

The dataset has two instances of the same kind labeled as chromosome. The prediction yields only one mask:

Tensorflow on old CPU

Just read Vikram Aggarwal' article: https://www.eggwall.com/2022/01/tensorflow-28-and-jax-0176-for-no-avx.html

Pig (Sus domesticus) karyotype: DAPI and labels

DAPI

Karyotype labels

p, q arms labels:

Loading the 125-COCO chromosomes dataset with ligthning flash: Notebook available on kaggle

Notebook on kaggle (choose version 2)