cells | BIII

EMPIAR

Read more about EMPIAR
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EMPIAR (https://empiar.org/ or https://www.ebi.ac.uk/empiar), the Electron Microscopy Public Image Archive, is a public resource for raw images underpinning 3D cryo-EM maps and tomograms (themselves archived in EMDB). EMPIAR also accommodates 3D datasets obtained with volume EM techniques and soft and hard X-ray tomography.

CXIDB

Read more about CXIDB
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The main goal of the Coherent X-ray Imaging Data Bank is to create an open repository for CXI experimental data.

Cell Image Library

Read more about Cell Image Library
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The Cell Image library is a large repository of images from all organisms, cell types, and processes, normal and pathological. Original format and ome-tiff format can be downloaded.

napari-pyclesperanto-assistant

Collection

Component

Description

The napari-pyclesperanto-assistant is a yet experimental napari plugin for building GPU-accelerated image processing workflows targeting life-sciences and bio-image analysis. It is part of the clEsperanto project. It uses pyclesperanto and pyopencl as backend for processing images.

has topic

Bioimage informatics

has function

Image analysis

Read more about napari-pyclesperanto-assistant
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DeepCell

Component

Description

DeepCell is neural network library for single cell analysis, written in Python and built using TensorFlow and Keras.

DeepCell aids in biological analysis by automatically segmenting and classifying cells in optical microscopy images. This framework consumes raw images and provides uniquely annotated files as an output.

The jupyter session in the read docs are broken, but the one from the GitHub are functional (see usage example )

has topic

Fluorescence microscopy

Phase contrast microscopy

has function

Cell segmentation

Cell tracking

Morphological operation