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 plays an increasing role in more and more research areas. Scientists find themselves doing the same analysis on multiple data sets over and over again.

Now there is a way to load multiple data sets, run a sequence of Imaris functions for each one and then get the resulting statistics and Imaris scene file back in an automated way.

Suitable for automated fluorescence microscopy and all repetitive imaging processes, ImarisBatch supports the following Imaris functions: spot detection, surface detection, tracking, various image processing functions, statistics output and Imaris scene file output. Batch processing jobs are typically generated by Imaris and registered with the batch job scheduler. A graphical interface enables you to combine jobs with lists of input files and output settings.

Batch processing has these benefits:

• Automation: by repeating certain procedures multiple times automatically, batch processing saves valuable time

• Reproducibility: Because ImarisBatch exactly reproduces procedures, it is easy to document what is completed for every image.

• ImarisBatch decouples time consuming procedures from interactive Imaris sessions, thus potentially freeing a copy of Imaris for use

• Batch processing allows sharing of computer resources among many researchers and shifts the time of job processing to when the computing resources are less busy.

• ImarisBatch can utilize large servers that have vast amounts of RAM memory and processors. Each job can be run on a separate processor provided there is enough RAM memory and the configuration of Imaris Batch purchased. Processing on multiple processors will speed the completion of all the batch jobs.

Features Include:

(1) Batchable Operations

ImarisBatch will access images directly and will not depend on Imaris. The following operations are accessible by both Imaris and ImarisBatch and hence are “batchable”. You will create the "Command sequence" (a Batch job) in an interactive Imaris session, which can also be saved. The Batch Coordinator will utilize the "Command Sequence" to complete the processing.

• Load Any Confocal Image

- Load any image from the file formats described on the Imaris product page.

• Preprocessing

- Crop
- Add / Delete Channels
- Add / Delete Time Points
- Change Voxel Size
- Change Time Stamps

• Image Filter / Processing

- Baseline
- Gauss
- Linear Stretch
- And Many More

• Image Analysis

- Detect Spots
- Detect Surfaces
- Track Spots And Surfaces

• Store Statistical Results

- Specify Output (file name)
- Specify Statistics Types

(2) Batch Job File

The “Batch job” is a collection of processing functions (command sequence) that is created in an interactive Imaris session and saved as a Batch job file. This file is then utilized by the Batch Coordinator to perform the batch processing.

• Batch Job File Characteristics:

(3) Batch Coordinator

The ImarisBatch coordinator is a stand-alone application that manages Batch jobs and starts and controls their execution.

• Batch Coordinator Configuration

- The ImarisBatch Coordinator can be installed on the computer that runs Imaris or may be installed on a computer (such as a server) that does not have Imaris installed.
- ImarisBatch does have a graphical user interface, therefore if it is installed on a server, the user must be provided with remote desktop access to the server to run ImarisBatch.
- The computer that runs ImarisBatch must have access to the file system on which both the images and the batch job text files reside.
- The ImarisBatch Coordinator must also have file system access to write the results of the batch processing.

• Batch Coordinator Functions

- Receive new Batch jobs directly from Imaris or via the saved command sequence
- Add or delete Batch jobs to a batch processing list.
- Start / pause / continue / stop jobs in the batch processing list.
- Visualize a list of jobs currently scheduled including status information for those jobs. (i.e waiting, started, cancelled, error, completed)
- Replicate job instructions (from a Batch job file) to a list of input files. Allowing the Batch job instructions to be quickly applied to a large number of files.
- Edit Batch jobs
- Slightly modify the parameters contained in the Batch job file without needed to return to an interactive session of Imaris. Allows for the “tweaking” of batch processing functions when applied to a large set of images.
- Generation of output file names for each Batch job and the location to write each output file on the file system.
- Provide pop-up-notification if a job finished or crashed
- Launch externals applications to inspect input / output data (using Imaris, or Excel)
- Open the Batch Coordinator from the system tray (system tray icon remains, if window is closed)

(4) Batch Agent

The Batch Agent is the actual worker engine. It does not contain a direct user interface and is controlled via the Batch Coordinator and the operating system scheduler. You do not even know that this service is running since it is completely controlled by ImarisBatch, but because of this design it provides you with some powerful functions:

• Multiple different users (with difference access rights) can run Batch jobs at the same time.

• Access control is provided (Tom cannot modify Peter's jobs)

• If a single job has a problem (crashes, error, etc) the Batch application does not crash, but can launch a new job to be processed.

• Controls to start, stop, pause, or cancel jobs

• Sequential or Parallel execution of Batch jobs can be completed depending on license configuration. This allows multiple Batch jobs to be run at the same time depending on the number of processors and system memory.

• Allows ImarisBatch to run on Mac and Windows

(5) Licensing Options

• Stand Alone – This licensing option allows ImarisBatch to be placed on Mac or Windows computer system. Imaris does not have to be present and this version of ImarisBatch does NOT use or depend on the licenses of Imaris. Stand alone ImarisBatch is available in the following configurations:

- Stand-Alone up to 2 parallel jobs
- Stand-Alone up to 4 parallel jobs
- Stand-Alone up to 8 parallel jobs
- Stand-Alone up to 16 parallel jobs
- Stand-Alone up to 32 parallel jobs

• Imaris Dependent – This licensing option allows Imaris batch to be placed on Mac or Windows computer system, but utilizes licenses of Imaris and its modules as part of its operation. For example, if you want to perform batch operations that require tracking and the output of the statistics from those tracks, this version of ImarisBatch would use the Imaris, Imaris MeasurementPro, and ImarisTrack licenses. The advantage of this option is that it is lower cost than the stand alone version. The Imaris dependent version of ImarisBatch comes in two configurations:

- Imaris dependent – up to 2 parallel jobs
- Imaris dependent – up to 4 parallel jobs