Barcode reading

This example uses an image of microscope slides arranged in a template. Each of the slides contains a DataMatrix barcode.

Objective: to read barcodes on microscope slides, rotate each slide to be in the correct orientation and to export cropped images.

This example will cover

  • barcode reading,
  • the Objects view,
  • rotating objects and
  • sorting boxes into rows and columns.

Preamble

  • Open Templates/sialidae.inselect_template

    • Specifies a higher-resolution thumbnail than used in previous examples - useful for reading and transcribing labels on slides
    • Exported crops are saved to TIFF files
    • More complex metadata validation

  • Load 4.Barcodes/Drawer_40b_w45a_45b_46_47a.inselect

  • Select 'Light background' in the 'Box colours' section of the toolbar

    • This alters the colours of the bounding boxes
    • We hope to automate this in a future release

  • Segment

Refine

There are 100 sockets but automatic segmentation has created 102 boxes. The two extra boxes are around small stickers at the top left and top right of the image. Some of the sockets do not contain slides but contain red markers that indicate the location:

Microscope slides

  • Remove the boxes around the stickers at the top left and top right
  • Remove the boxes around the red markers

Once refined, we have 95 bounding boxes:

Microscope slides

Metadata template

Open Templates/sialidae.inselect_template in your text editor

  • The catalogNumber field contains Regex parser: '^[0-9]{9}$'

  • This is a regular expression that specifies the field should contain exactly nine digits with no letters or punctuation

  • If you do not know what a regular expression is, do not worry

Setup barcode reading

Select 'Configure' from the 'Barcodes' section of the toolbar:

Barcode reading options

  • Inselect comes with two open source options
  • The Commercial Inlite ClearImage is faster and is more reliable at reading barcodes
    • Windows only
    • Costly but you can run it for a short time with an evaluation license
    • If you are on Windows

Read barcodes

Read barcodes with F7.

  • Takes a few minutes to complete
  • We are asking quite a lot of the barcode reader - the barcodes make up about 1% of the area of each crop
  • Values of barcodes are always put into catalogNumber field

Other metadata

You will select the relevant groups of slides and set their values of location and genus.

Reminders

  • You can select bounding boxes with left-click and drag
  • You can add / remove individual boxes to / from the selection by holding down CTRL and left-clicking

Once completed, all metadata should be valid with all boxes clear:

Completed slides

Sorting boxes

You can sort boxes either by rows or columns.

  • Press CTRL + N a few times and see how selected box changes
  • Now click 'Into columns' in the 'Sort boxes' section of the toolbar
  • Press CTRL + N a few times again

The selected sort option is applied when you segment an image.

Objects view

Switch to the Objects view.

Some relevant shortcuts

  • CTRL + 1 / CTRL + B - selects the Boxes view
  • CTRL + 2 / CTRL + J - selects the Objects view
  • Can switch between views using
    • CTRL + PgUp / CTRL + PgDown on Windows
    • CMD + [ / CMD + ] on Mac

This view shows crops on a grid with a square for each bounding box, along with each box's number and object label:

Completed slides

  • You can expand a single box

    • press Enter
    • double click
    • CTRL + E

  • Move forwards and backwards through boxes

    • up and down arrows
    • CTRL + N and CTRL + P - Next / Previous

  • You can go back to the grid

    • Press Enter
    • Double click
    • CTRL + G

Selection

  • You can select icons with left-click and drag of the mouse
  • You can select icon using SHIFT + arrow keys
  • As you might expect CTRL + A and CTRL + D - the standard shortcuts for Select all and Select none - also work here
  • Just as before, the metadata fields reflect the selection

Rotation

You will rotate each crop so that labels are in the correct orientation.

  • CTRL + R to rotate right
  • CTRL + L to rotate left
  • Rotation is applied to the current selection, so you can block-select and rotate
  • Very uuseful for reading labels
  • Rotation is applied to crops so when they are saved

Rotated slides

Export crops

Click 'Save crops' and open the directory containing the crops.

  • The format of the filenames is defined from metadata template
  • Crops are saved to TIFF files, as specified in the metadata template
  • Crops are saved with the rotation the you specified