ImarisBatch - Software To Batch Process Microscopy Images | Imaris
 

ImarisBatch

ImarisBatch is an Imaris subsystem for the processing of 2D, 3D, and 4D image series in batch. This subsystem saves valuable time when running repetitive jobs because processing can be queued and completed without interaction from the user. Since the introduction of Imaris 8.0 batch operations can be triggered directly from the Arena view. The user can execute a pre-defined image analysis protocol on all images of one group or all images from multiple groups. The results of batch analysis can be directly displayed and explored in Imaris Surpass or Imaris Vantage.

  • Save valuable time by batch processing
  • Reproduce exact analytical procedures
  • Decouple time consuming procedures from interactive sessions
  • Batch process the full experiment and get the results which preserve the experiment structure
  • Utilize large servers for parallel processing

Automation and Reproducible Way of Analysing an Experiment

Recent technical advances in fluorescence microscopy provide faster and more detailed information about cells, subsets of cells and about structures, molecules and proteins within cells. Given the growing quantity of information, automation of data analysis is a crucial step in the process of scientific discoveries. What plays an increasingly important role in image analysis are also reproducibility and a reliable way of creating comparisons between experimental groups.

ImarisBatch is a powerful module which can solve both problems at the same time. Using ImarisBatch saves valuable time as once you create an image analysis protocol (Spots, Surfaces, Cells, Filaments) it can be used on an unlimited number of images. As all datasets are analysed with the same parameters, without user influence, this approach guarantees reproducibility and comparability of the results within one group or between multiple experimental groups. Those are the key factors for a systematic scientific approach which make the measurements and comparisons more valuable.

Batchable Operations and Workflow

ImarisBatch is now fully integrated into Imaris and you can run the operations directly from the Arena view on images within a selected group or group tree. The following operations are accessible by both Imaris and ImarisBatch and hence are “batchable”:

  • Detect Spots
  • Detect Surfaces
  • Detect Cells
  • Detect Filaments
  • Track Spots, Surfaces, Cells and Filaments

The first step of the ImarisBatch workflow is creation of the image analysis protocol for Spots, Surfaces, Cells or Filaments and saving the creation parameters in the selected group in Arena. Those creation parameters can be then used to analyse all images in the selected group or multiple groups within the Arena view with just one click “Run Batch Job”. This way the user can analyse the full experiment (including control and experimental groups) and get the results immediately.

The Imaris Batch output can be accessed and investigated in the following ways:

  • New objects are added to a dataset and can be opened and explored in Imaris Surpass View
  • The collection of Batch results can be explored in Imaris Vantage
  • All statistics can be exported as a full .xls report

Batch Agent and ImarisCommander

The Batch Agent is the actual worker engine which is started from the Arena view when you select “Run Batch Job” operation. The Batch Agent coordinates processing of all images in the group by running the ImarisCommander application for each image. Each Imaris Commander application runs on one or more cores, depending on the process (most Imaris functions are multithreaded). There can be up to four ImarisCommanders running at the same time. Once the Batch Agent is started and the operation of batch processing images is in progress, the user can continue working in Imaris as usual (all module licenses are available).

Licensing Options

ImarisBatch is an optional Imaris module which is started and controlled directly from the Arena view. The ImarisBatch licensing option allows it to be used on Mac or Windows computer system and it does NOT use or depend on the other module licenses of Imaris – if you have a protocol (creation parameters made in any of the Imaris modules) saved on your disk, you can batch process the images even though the license is not physically present on the machine. However, to visualize the results you’ll need the module license.

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