Support

3DEM TOMOGRAPHIC RECONSTRUCTION:

Transform-based Tracking, Bundle Adjustment and Reconstruction (TxBR):  Software for 3D image acquisition and reconstruction of electron microscopic tomography (EMT) datasets.  Accommodates effects of curvilinear electron trajectories, sample warping, point spread functions (PSF), errors in alignment, noise, and the missing cone of projections. Supports reconstruction from various schemes of data acquisition, notably multiple tilt series of the same region of interest, acquired at different clocked orientations about the optical axis.

• https://github.com/nbcrrolls/txbr-source 

3DEM IMAGE SEGMENTATION:

Cascaded Hierarchical Model (CHM): Provides a scalable solution for the automatic segmentation of images, including natural scene processing and cellular structures in electron microscopy data.

• https://github.com/slash-segmentation/CHM

• https://github.com/CRBS/chm_singularity

• https://github.com/CRBS/chmutil

CDeep3M: A plug-and-play, cloud-based deep learning solution for the automatic segmentation of light, electron and X-ray microscopy data sets.

• https://github.com/CRBS/cdeep3m 

Probability Map Viewer: A web application for viewing probability map generation in near real time on tiled image data.

• https://github.com/CRBS/probabilitymapviewer 

Segmentation Utilities: Post-processing tools for masking segmented features, manipulating IMOD model files, and performing organelle specific morphometric analysis.

• https://github.com/CRBS/segmask

• https://github.com/CRBS/PyIMOD

• https://github.com/CRBS/morphome

IMOD Utilities: NCMIR developed plugins for IMOD for manually tracing contours, performing stereology, and facilitating volumetric data analysis.

• drawingtools.html

• stereology.html

• stereology_help.html

• analysistools.html

• beadhelper.html

• grabslicer.html

• interpolator.html

• namewizard.html

• naming_help.html

   

MULTICOLOR ELECTRON MICROSCOPY:

multicolor_em: NCMIR developed ImageJ plug-in for overlaying correlated, color-coded nanoSIMS/EELS chemical maps atop conventional EM images.  Refer to “Multicolor Electron Microscopy for Simultaneous Visualization of Multiple Molecular Species.” Cell Chemical Biology, 2016 for additional details.

• https://github.com/CRBS/multicolor_em

CELL IMAGE LIBRARY (CIL): 

The CIL is a NCMIR maintained, public resource database of images, videos, and animations of cells, capturing a wide diversity of organisms, cell types, and cellular processes. The purpose of this database is to advance research on cellular activity, with the ultimate goal of improving human health.

Cell Image Library Website:  The CIL website is the public interface to the database.  Features include general keyword search, advanced ontology assisted search, interactive visual cells, and multiple image display browsers. The CIL utilizes an Elasticsearch based NoSQL JSON search engine.

• https://github.com/CRBS/CIL_PHP_Website

CIL Rest API: This API allows the CIL website to retrieve and find documents from the Elasticsearch JSON search engine.

• https://github.com/CRBS/CIL_RS

NCMIR Tools: Command Line Tools for interacting with the NCMIR/CIL hosted filesystem.

• https://github.com/CRBS/ncmirtools

CIL Image Viewer (Public): Web-based, multi-resolution image stack (volume) browser.

• https://github.com/CRBS/CIL_Image_Viewer

CIL Image Viewer Data Convertor: Scripts for processing image volumes into the multi-resolution format compatible with the CIL Image Viewer.

• https://github.com/CRBS/Image_Viewer_Data_Converter