Scale Bars

Cytosketch provides a tool to add and adjust scale bars and to calibrate images. To add scale bars, select the images to add a scale bar to and click the Scale Bar Tool button Scale Bar button. Cytosketch automatically adds an appropriately sized scale bar to each of the selected images. Controls are available to adjust the appearance of the scale bar and to set the length (μm) that the scale bar represents.

Cytosketch takes care of updating the number of pixels that are required to draw the scale bar whenever the image is calibrated, cropped, resized or the scale bar size is changed.

To calculate the correct number of pixels, the spatial calibration (pixels/μm) of the image is required. Where possible, Cytosketch reads this data from the image file while the image is imported. If the spatial calibration was not read, a simple tool is available to manually calibrate your images. For more information regarding adding scale bars to un-calibrated images have a look at the Adding Scale Bars to Uncalibrated Images section.

Cytosketch currently extracts the spatial calibration from images taken on some confocal microscope. Please contact us at info@cytocode.com, if your image file contains this information but Cytosketch does not read it.

This section describes how to add and adjust scale bars and explains how to calibrate images in order to get an accurate scale bar.

Table of Content

Scale Bar Controls Overview

This section provides a quick overview of the controls that are available in the Scale Bar Tool box. Move the mouse over the screen shot below to see a short description of the individual controls or over the description to see the corresponding controls on the screen shot.

Scale Bar Controls magnification calibration manage Set scale bar reset scale bar apply scale bar
  1. Control to set the magnification with which the image has been taken.
  2. Control to set and add spatial calibration for the selected image.
  3. Control to manage the list of spatial calibrations.
  4. Control to set the size of the scale bar shown on the image.
  5. Resets the scale bar to an appropriate size for the selected image.
  6. Applies the spatial calibration of the image with the focus to the rest of the selected images.

Adding Scale Bars

It's easy - select the images to add scale bars to and click the Scale Bar Tool button Scale Bar button.

Set the Size of the Scale Bar

  1. Activate the scale bar tool by double clicking the scale bar or by selecting the image and then clicking the Scale Bar Tool button Scale Bar button.
  2. Click Set next to Bar Size and enter the desired scale bar size in the dialog that appears.
  3. The scale bar size is adjusted after you click Ok.

Reset the Size of the Scale Bar

  1. Activate the scale bar tool by double clicking the scale bar or by selecting the image and then clicking the Scale Bar Tool button Scale Bar button.
  2. Click Reset next to Bar Size and the size of the scale bar is set to an appropriate size for the selected image.

Changing the Appearance of the Scale Bar

  1. Select the scale bar by using the selection tool.
  2. Click on the drop down list in the Style box and select a new style from the list.

Adding Scale Bars to Uncalibrated Images

To calculate the correct number of pixels that are required to draw the scale bar, the spatial calibration data of the image is required. The spatial calibration data is the number of pixel per μm for a specific magnification and microscope. Where possible, Cytosketch reads this data from the image file while the image is imported. If the spatial calibration was not read, you can manually calibrate your images.

Cytosketch provides a simple tool to calculate the calibration data using images that contain an object of a known size (image of stage micrometer or scale bar). Each new calibration data that is added to Cytosketch is automatically saved. To keep the calibration data organized, calibration data from the same microscope are grouped together.

Adding New Calibration Data

Follow the steps below to add scale bars to uncalibrated images:

  1. Select the images to add a scale bar to and then click the Scale Bar Tool button Scale Bar button.
  2. In the Scale Bar Tool box, set the image magnification by selecting the appropriate magnification from the drop down list. Skip this step if the magnification is already correct.
  3. Scale Bar Tool box Magnification
  4. Click on the drop down list next to Calibration and select New.
  5. Scale Bar Tool box
  6. In the dialog that appears load an image that contains an object of known size and measure a distance with the provided ruler.
  7. Enter the name of the microscope that the image was taken on, the image magnification and the distance that was measured. After you click Ok, an appropriate sized scale bar is added to each of the selected images and the calibration data is saved.
  8. The next time you need add scale bars to uncalibrated images, just select the appropriate calibration data from the drop down list.
  9. Scale Bar Tool box saved calibration data

Below is a short movie that shows how to add scale bars to uncalibrated images.

Adding Scale Bars in Bulk

Cytosketch lets you add scale bars to images with different magnification at the same time. To add the correct sized scale bar to these images, select the microscope from the calibration list instead of the individual calibration data.

Cytosketch automatically calibrates the images using the calibration data that is stored with the selected microscope. For each image, the calibration data that has a magnification that is closest to the image magnification is used.

If the calibration data and the image to calibrate do not have the same magnification, Cytosketch automatically adjusts the calibration data.

Follow the steps below to add scale bars to multiple images at the same time:

  1. Select the images to add a scale bar to and then click the Scale Bar Tool button Scale Bar button.
  2. In the Scale Bar Tool box, set the image magnification by selecting the appropriate magnification from the drop down list. Skip this step if the magnification is already correct.
  3. Scale Bar Tool box Magnification
  4. Click on the drop down list next to Calibration and select a microscope.
  5. Scale Bar Tool Box Mic
  6. An appropriate sized scale bar is added to each of the selected images.

Steps to Delete a Spatial Calibration:

  1. Select an image and then click the Scale Bar Tool button Scale Bar button.
  2. In the Scale Bar Tool box, click Manage.
  3. Scale Bar Tool box Manage
  4. In the dialog that appears select a microscope.
  5. Close the calibration image tab to delete the spatial calibration.

Calibrate From Selected Image

If your image contains a scale bar that was added with another software and you do not need the spatial calibration data for other images, calibrate your images using From Selected Image.

  1. Select the image to add a scale bar to and then click the Scale Bar Tool button Scale Bar button.
  2. In the Scale Bar Tool box, set the image magnification by selecting the appropriate magnification from the drop down list. Skip this step if the magnification is already correct.
  3. Scale Bar Tool box Magnification
  4. Click on the drop down list next to Calibration and select From Selected Image.
  5. Scale Bar Tool box
  6. In the dialog that appears, the selected image is automatically being loaded. Click the Load Image button if another image is required
  7. Measure a distance with the provided ruler and enter this distance.
  8. After you click Ok, an appropriate sized scale bar is added to the selected images and the calibration data is saved to the image metadata.