danielmoraisg/count_cells

Fast ai based project to count cells from microscopy images

Count_cells

Fast ai based project to count cells from microscopy images

Objective

The aim of this project is to facilitate life of those researcher who have to spend hours counting cells on a microscope

How??

To achieve this objective a machine learning algorithm is going to do all the hard work for yourself. The algorithm is a pytorch/Fastai python script that enables a resnet archtecture to learn how to count cells in an image

datasets

The dataset used to train both neural networks is a kaggle dataset called Broad Bioimage Benchmark Collection under the accesion number BBBC038

Notebooks

The notebook entitled count_cells 2 is a first approach to the problem. it uses a resnet 50 to learn how to segmentate images and a resnet38 with some changes in the layers to learn how to count the number of the cells. The changes in the layers were based on a notebook that creates an image regression model based on Fastai library

count_cells's Issues

pretrained model

Hello and thank you for sharing your work!
Could you please provide the last checkpoint for the pretrained model?
Thank you in advance, Lucia