v2.0

by Joana Raquel Delgado Martins

Imaris Part 1: File conversion and opening files

Written By: Joana Raquel Delgado Martins
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Difficulty

Easy

Steps

7

Time Required

00:05:00

Sections

1

Flags

0

Introduction

Imaris requires IMS files as input. Imaris File Converter can be used to convert your files into *.ims so you can visualize them in Imaris.

  1. Reserve and open a ZMB image processing virtual machine.

    • Reserve and open a ZMB image processing virtual machine.

    • Open ImarisFileConverter.

  2. Either Drag & Drop the files you wish to convert, or click "Add Files...". Either Drag & Drop the files you wish to convert, or click "Add Files...".

    • Either Drag & Drop the files you wish to convert, or click "Add Files...".

  3. If you have *.lif (Leica) files containing 2D and 3D you might be asked to change the voxel size. Imaris 9.9 is not able to handle LIF files with mixed 2D and 3D datasets.

    • If you have *.lif (Leica) files containing 2D and 3D you might be asked to change the voxel size.

    • Imaris 9.9 is not able to handle LIF files with mixed 2D and 3D datasets.

    • If your files have different z step sizes this change will affect all your files!

    • You can hoover over your file name to check the dimensions of the different datasets.

    • Until this bug is fixed please use the workaround of doing the conversion in Imaris Arena.

  4. It is recommend that you save your processed files in a different folder than your raw data. Click "Specific Folder:".

    • It is recommend that you save your processed files in a different folder than your raw data.

    • Click "Specific Folder:".

    • Choose the desired folder path.

  5. Multiple files of a series such as 3D stacks, time series and multi channel images should be automatically recognized as a single *.ims file. If the dimensions are not properly detected you can select your file and click on "Settings". Here you can adjust the dimensions of the image series for conversion.

    • Multiple files of a series such as 3D stacks, time series and multi channel images should be automatically recognized as a single *.ims file.

    • If the dimensions are not properly detected you can select your file and click on "Settings".

    • Here you can adjust the dimensions of the image series for conversion.

    • In the example each file correspond to a different channel (C). The same principle would apply to different Z planes (Z) or timepoints (T).

    • For container files such as .lif (which can contain multiple images/datasets) an individual *.ims file for each image/dataset will be generated.

  6. You can now start converting your files by pressing "Start All". If the conversion is successful you will now see a green mark next to your files.

    • You can now start converting your files by pressing "Start All".

    • If the conversion is successful you will now see a green mark next to your files.

  7. Open your specified folder and double click to visualize your file. Alternatively you can also use the Arena view in Imaris to browse through the different files. Please check the corresponding guide.

    • Open your specified folder and double click to visualize your file.

    • Alternatively you can also use the Arena view in Imaris to browse through the different files. Please check the corresponding guide.

Finish Line

Author

Joana Raquel Delgado Martins

Member since: 04/09/2019

3,552 Reputation

39 Guides authored

Team

ZMB Staff Member of ZMB Staff

11 Members

129 Guides authored

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