Import images

Its important to be able to incorporate images into the experimental record -- that's why eCAT has makes it easy to get your images into records. eCAT also supports a wide range of file formats, including special scientific formats. And that's a lot easier than printing off the images and pasting them into a paper labbook!

Adding an image is really easy. You can just upload it from your local computer when you are editing, and the image will appear in your record like in the screenshot below.

As well as adding an image to a record, you can also import a images as their own records. The data that will be imported is detailed below.

zeiss

01. Import
Zeiss LSM Confocal

Carl Zeiss confocal microscopes such as the LSM 510 Confocal Microscope produce LSM files. These are are binary files which store images - and also the 'Short' and 'Detailed' notes, and the settings of the microscope.

The importer reads all the standard image-related metadata from LSM files into a record of class "LSM File" and metadata for tracks and lasers into subrecords of it. Subrecords are also created for each plane in the image stack, with each subrecord containing the dimensions of that plane and the thumbnail.

zvi

02. Import
Zeiss ZVI Confocal

ZVI files are also developed by Zeiss for confocal imaging. The format groups together your mage data with all relevant information in a compact file with data including acquisition date, microscope settings, exposure values, size and scale details, fluorescent dyes used and more.

The importer reads all the standard image-related metadata from ZVI files into a record of class "ZVI File" and metadata for planes into subrecords of it. Subrecords are also created for each plane in the image stack, with each subrecord containing the dimensions of that plane and the thumbnail.

biorad

03. Import
Biorad Confocal

The Biorad Confocal importer imports files from a Biorad MRC 600 confocal microscope. In addition to reading the standard image metadata into a record of class "Biorad File", the importer reads Lens and Frame Interval settings and reads in the optional "notes" at the end of pic files as name / value pairs.

leica

04. Import
Leica Confocal

The Leica Confocal importer imports files from a variety of Leica microscopes. These files consist of a binary .lei file that describes how a collection of related tiff files can be combined to display the microscope images.

Leica files can contain multiple image stacks in a single file and the main thumbnail image in the "Leica File" class always displays a single image per image stack per file. This image is a Z projection of the stack. The children of the imported record display the records of class "Leica Image" that represent each image stack. Instances of "Leica Image" classes contain a single thumbnail of the Z projection of the stack and a list of subplanes which display thumbnails of each channel for each plane in the stack. They also contain subrecords containing the metadata describing that image stack in the Dimension, Hardware, Scanner, Timestamps and LUT fields.

deltavision

05. Import
Deltavision

Deltavision is Applied Precision's microscope system designed to acquire and deconvolve multi-dimensional images of fluorescently-labeled specimens. Catalyzer can read Deltavision raw (.DV) and deconvolved (.R3D) files.

The Deltavision Importer generates "Deltavision File" records which contain the thumbnail of the image stack as well as a lot of metadata from the Deltavision file including a summary of the image and image acquisition parameters (time series, Z plane settings and wavelengths acquired).

metamorph

06. Import
Metamorph

The MetaMorph Imaging System is a product from the Universal Imaging Corporation that automates image capture and analysis from scientific grade digital CCD cameras.

The MetaMorph Importer generates "MetaMorph File" records which contain the thumbnail of the image stack as well as a lot of metadata from the metamorph file. The list of planes is represented as a list of records of class "MetaMorph Plane" and each of these contains a large amount of metadata specific to that plane and a thumbnail of the plane.

iplab

07. Import
IPLab

IPLab is Scanalytics Inc's image acquisition, processing, measurement, and analysis software. Catalyzer imports IPLabs ipl files and generates a main thumbnail of its image stack as well as subrecords containing an image of each thumbnail in the plane. Both a summary of the experiment, image and image acquisition parameters (time series and Z plane settings, camera and filter settings) and detailed information on the same parameters are imported.

tiff

08. Import
TIFF

TIFF is a standard image format that can be generated by many image acquisition and image manipulation systems.

The "TIFF File" record that is created on import contains a list of "TIFF Planes" each of which contains the metadata for that plane of the image stack. Each plane record contains a image of that plane and the "TIFF File" record contains a summary image.

jpeg

09. Import
JPEG

JPEG is a standard image format that can be generated by many image acquisition and image manipulation systems.

The "JPEG File" record that is created on import contains a thumbnail of the image in the file and the basic image metadata. In addition if EXIF (Exchangeable Image File Format), IPTC (International Press Telecommunications Council) or GPS (Global Positioning System) metadata is present, this will be read into subrecords. Digital cameras often create this sort of metadata.

eCAT is a flexible, easy to use electronic lab notebook that lets you add structure to your lab's research data in an integrated collaborative online environment.