Method and apparatus for automated cellular bioinformatics

Abstract

An automated system that conducts, monitors, and validates a cell-line-based biological experiment including one or more treatment compounds or other external stimuli. In one preferred embodiment, the system comprises two principal subsystems, and optionally accessory subsystems. A first principal subsystem is an automated laboratory experiment manager for designing the biological experiment, for constructing an assay plate used to conduct the biological experiment, and for managing one or more of the processes that constitute the biological experiment. A second principal subsystem is an automated data analysis manager for analyzing images, for instance produced by the image production system, to detect image data including biological markers and objects, for analyzing the resulting image data to produce biological data, and for analyzing the biological data to produce biological phenotypes and treatment compound signatures.

1 . An automated system for analyzing cellular images comprising: 
 (a) a plurality of feature extractor subsystems to extract features from images of assay plate wells, the features to be used in image analysis tasks;    (b) a supervisor subsystem for facilitating storage and retrieval of the images and coordinating feature extractors processes through message queues;    (c) a source of algorithms, each algorithm associated with an image analysis task;    (d) a source of input data; and    (e) an algorithm subsystem to interface with the source of algorithms and the source of input data.    
   
   
       2 . The system of  claim 1 , wherein the image analysis tasks characterize a cellular organelle, a material in the cell, or a combination thereof.  
   
   
       3 . The system of  claim 2 , wherein the image analysis tasks are selected from the group comprising determining the shape of a cell, characterizing the nucleic acid of a cell, characterizing the Golgi of a cell, and combinations thereof.  
   
   
       4 . The system of  claim 1 , wherein the feature extractor subsystems perform the image analysis tasks.  
   
   
       5 . The system of  4 , wherein the supervisor subsystem allocates image analysis tasks across the feature extractor subsystems.  
   
   
       6 . The system of  claim 4 , wherein the feature extractor subsystems perform the image analysis tasks in parallel.  
   
   
       7 . The system of  claim 1 , wherein each feature extractor subsystem comprises one or more individual servers.  
   
   
       8 . An automated method for analyzing a plurality of cellular images, the method comprising: 
 (a) generating a plurality of assay plate well image files;    (b) storing the image files in a depository;    (c) registering the image files with a database;    (d) identifying a plurality of image analysis tasks;    (e) for each identified image analysis task, selecting a feature extractor to handle the task;    (f) for each identified image analysis task, inputting one or more of the registered image files; and    (g) performing the identified image analysis tasks in parallel on the selected feature extractors.    
   
   
       9 . The method of  claim 8 , wherein a supervisor software entity identifies the image analysis tasks and selects the feature extractors.  
   
   
       10 . The method of  claim 8 , wherein a supervisor software entity stores and registers the image files.  
   
   
       11 . The method of  claim 8 , further comprising, for each identified image analysis task, identifying an algorithm to extract features from the image files as part of the image analysis task.  
   
   
       12 . The method of  claim 11 , further comprising importing the identified algorithm into the selected feature extractor for execution.  
   
   
       13 . The method of  claim 8 , wherein the image analysis tasks characterize a cellular organelle, a material in the cell, or a combination thereof.  
   
   
       14 . A method for designing and conducting a biological experiment comprising: 
 a) designing a biological experiment;    b) automatically generating processes to conduct the experiment;    c) constructing an assay plate used to conduct the biological experiment; and    d) automatically managing one or more of the processes to conduct the experiment.    
   
   
       15 . The method of  claim 14 , further comprising generating an image of at least a portion of at least one well of the assay plate.  
   
   
       16 . The method of  claim 14 , wherein at least some of the processes are selected from the following: plating processes, washing processes, fixing processes, staining processes, imaging processes, DNA analysis processes, non-DNA analysis processes and fluidics processes.  
   
   
       17 . The method of  claim 14 , further comprising automatically tracking a cell line used in the experiment.  
   
   
       18 . The method of  claim 14 , further comprising automatically tracking a reagent used in the experiment.  
   
   
       19 . The method of  claim 14 , further comprising automatically tracking a treatment compound used in the experiment.  
   
   
       20 . The method of  claim 14 , wherein designing the biological experiment comprises entering parameters defining the experiment using a user interface.