Bisque (Bio-Image Semantic Query User Environment) : Store, visualize, organize and analyze images in the cloud. It also allow to run workflows using a set of deployed tools, such as CellProfiler, RootTipMultin Nuclear Tracker, Microtubule tracker etc...

Bisque was developed for the exchange and exploration of biological images.

The Bisque system supports several areas useful for imaging researchers from image capture to image analsysis and querying. The bisque system is centered around a database of images and metadata. Search and comparison of datasets by image data and content is supported. Novel semantic analyses are integrated into the system allowing high level semantic queries and comparison of image content.

  • Bisque is free and open-source
  • Flexible textual and graphical annotations
  • Cloud scalability: PBs of images, millions of annotations
  • Distributed storage: local, iRODS, S3
  • Integrated image analysis, high-throughput with Condor
  • Analysis in MATLAB, Python, Java+ImageJ
  • 100+ biological image formats
  • Very large 5D images (100+ GB)
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bisque screenshot



OpenImadis stands for Open Image Discovery: A platform for Image Life Cycle Management. It was previously called CID iManage (for Curie Image Database).

No image data conversions, no duplication.

- Uploads data to a secure server in the original format

- Unique id for data

Supports sharing and collaboration with access control

- Allows users to upload, view, update or download data based on their access privileges

Supports multiple ways of attaching meta-information

- Annotations, comments and file attachments

-Analysis results as query-able visual objects

Supports Archiving (data moving to another long-term storage but still searchable)

Facilitates custom visualization and analysis

- Access data from preferred analysis and visualization tools

- Access relevant bits of data to build efficient web and mobile application

Facilitate easy access to analysis and visualization applications hosted on other servers

- Run analysis on dedicated compute clusters

- Access applications hosted and published by other users

Highly Scalable

- Supports on-the-fly addition of server nodes to scale concurrent usage




Fit a model for the growth of yeast cells


This notebook uses the rOMERO-gateway and EBImage to process an Image associated to the paper 'Timing of gene expression in a cell-fate decision system'.

The Image "Pos22" is taken from the dataset idr0040-aymoz-singlecell/experimentA/YDA306_AGA1y_PRM1r_Mating. It is a timelapse Image with 42 timepoints separated by 5 minutes. This Image is used to fit a model for the growth of the yeast cells. The notebook does not replicate any of the analysis of the above mentioned paper.

Its purpose is mainly to demonstrate the use of Jupyter, rOMERO-gateway and EBimage.


What it does:

  • For each time point of one movie:
    • Read the image for this time point  from the IDR
    • Threshold the images and count the cells using EBimage functions
  • Fit an exponential model to the count of cells against time to get a coefficient of grow (exponential factor)




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Cell or particle Counting and scoring stained objects using CellProfiler


This is a Jupyter notebook demonstrating the run of a code from IDR data sets by loading a CellProfiler Pipeline 

The example here is applied on real data set, but does not correspond to a biological question. It aims to demonstrate how to create a jupyter notebook to process online plates hosted in the IDR.

It reads the plate images from the IDR.

It loads the CellProfiler Pipeline and replace the reading modules used to read local files from this defaults pipeline by module allowing to read data remotely accessible.

It creates a CSV file and displays it in the notebook.

It makes some plot with Matplotlib.



Quantification of outer ring diameters of centriole or PCM proteins of cycling HeLa cells in interphase


This workflow can be ran with data from 3D-SIM showing the centrosomes in order to compare the distribution of diameters of rings (or toroids) of different proteins from the centrioles or the peri centriolar material. It aims to reproduce the results of the Nature Cell Biology Paper Subdiffraction imaging of centrosomes reveals higher-order organizational features of pericentriolar material  from the same data set but with a different analysis method.

It is slightly different from the methods described in the paper itself, where the method was to work on a maximum intensity projection of a 3D-SIM stack, and then to fit circle to the centrioles to estimate the diameters of the toroids.

In this workflow, the images are read from the IDR , then process by thresholding (Maximum entropy auto thresholding with Image J), and processed by Analyze Particles  with different measurement sets, including the bouding box. Then the analysis of diameters and the statistical test are performed using R. All the code and data sets are available, and in the case of this paper have shown a layered organisation of the proteins.

Combined view from Figure 1 Lawo et al.



Classification of trajectoire: need tracking results as input and will then classify the trajectories as  brownian motion, confined brownian or directed.

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intelligent Matrix Screener Remote Control


Integrates hardware control of Leica microscopes (via CAM), image analysis (e.g. via ImageJ, Matlab), and adaptive automatic screening of identified regions of interest.



Scipion is an image processing framework for obtaining 3D models of macromolecular complexes using Electron Microscopy (3DEM). It integrates several software packages and presents a unified interface for both biologists and developers. Scipion allows you to execute workflows combining different software tools, while taking care of formats and conversions. Additionally, all steps are tracked and can be reproduced later on.



WormGUIDES Atlas is an interactive 4D portrayal of neural development in C. elegans. It will ultimately contain nuclear positions for every cell in the embryo, identified and tracked from the 2 cell stage until hatching. Single-cell and subcellular information, including neural outgrowth dynamics for each cell as well as cell function, gene expression, the adult neural connectome and related literature will be collated for each cell from public sources and also integrated with the atlas model. WormGUIDES Atlas integrates tools for exploratory data analyses and insight sharing. Navigation is linked between 3D and lineage tree views. In both contexts, community single cell information can be accessed with a click, creating live web queries that summarize knowledge about a cell. In many cases this information can be used to control cell color, creating customized interactive visualizations. A user's insights can be annotated directly into the embryo model with a note-taking interface that attaches each annotation to a cell or other point in space and time. These multi-dimensionally located notes can then be ordered into a (chrono)logical story sequence that explains developmental events as they unfold in the embryo. Annotations can be saved and shared with collaborators or the community.

WormGuides screenshot

Focal Adhesion Analysis Server


The website implements a set of computer vision algorithms designed to automatically process time-lapse images of fluorescently labeled focal adhesion proteins in motile cells. The methods associated with the processing have been published in PLOS One and Cell.

The publication describes a quantitative analysis of focal adhesion dynamics that have been imaged using TIRF. All image processing steps are well explained or referenced.

To better understand the dynamic regulation of focal adhesions, we have developed an analysis system for the automated detection, tracking, and data extraction of these structures in living cells. This analysis system was used to quantify the dynamics of fluorescently tagged Paxillin and FAK in NIH 3T3 fibroblasts followed via Total Internal Reflection Fluorescence Microscopy (TIRF). High content time series included the size, shape, intensity, and position of every adhesion present in a living cell. These properties were followed over time, revealing adhesion lifetime and turnover rates, and segregation of properties into distinct zones.

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