Imaging Records

When imaging, we need to record enough information to find the images we need, know what we're looking at when viewing an image, be able to reproduce the image or acquire other images in the same way, and of course to describe all relevant details in a manuscript's  methods section. Below is a detailed list of information to be recorded with explanation of the entry, which we may want to use to create a printable template or a Google document form.

Layout: Organizing the record into sections (Header, Source, Content, Acquisition, and File Info) will help ensure all info is recorded and make it easier to find things and compare settings across images and session.

Session Header 
This section contains information that applies to the entire session. Part is entered at the start of the session, and the part at the end of the session.

• Date
• Microscope
• What is being imaged (immuno and brain region)
• Total # of images acquired
• Range of file #'s of related images (e.g., same brain region, but different objective or acquisition parameters)

Image Source 
Imaging source information is recorded after the header and for each image as needed. That is, if the imaging session is organized the Image Source info can organize the record into sections, making it easy to add the summary info at the end of the session.

• Experiment (the immuno run and date; should be the 1st two lines on the slide)
• Brain and series (e.g., G1110c)
• Section # in either/both relative o/andr absolute notation. Relative notation refers to slide and section (e.g., 2-3 for first slide, third section). Absolute notation refers to the nth section of the entire series (e.g., S23, which is probably the 5th section on the 4th slide (4-5)). Relative numbering makes it easier to find the slide. Absolute numbering helps keep slides in register across series. For the LHA immuno series, the absolute section numbers will be noted on the slide

Image Content

• Image number (Starting with Image 01. Number consecutively for all images acquired in the session)
• Immuno and labeling (What's labeled and what it's labeled with; e.g., ms∝NOS (Cy2), rb∝NT (Cy3))
• Brain region imaged
• Objective (10X, 20X, etc.)

Note that this information can be combined into a sentence, e.g., 

Image 01 Tiled, 10X image of NOS/NT (Cy2/Cy3) in the LHA

Image Acquisition

• Channels. For each channel note

• Laser line(s) or Fluorescence Filter(s). 

• Laser Power for each line

• Scan Speed (6 - 8, usually 7)
• Averaging (1, 2, or 4)
• Aperture in Aiery (e.g., 1 or 1.51, etc.), in µm and slice thickness (in µm).
• Gain
• Offset
• Tiles (e.g., 3 X 4)
• Slices (number and slice thickness in µm)
• Acquisition Time (per tile and for entire image)

File Info

• Dimensions (generally 1024X1024 per channel)
• Bit depth (8 bit for now)
• File name. File naming should be date_image #_image content e.g.,

121001_01_LHA_Cy2NOS Cy3NT.cvi

or

121001_01_LHA_Cy2NOS Cy3NT_10X_9 tile_3 z.cvi

• File name of export. All files should also be exported as an OME.tif. The file name will generally be the same as above, but appended with the new file type
• Storage Location. Initially files will be stored on the same computer where acquired but at the end of the session a copy of all files should be made and transferred to a yet to be determined storage location.