EXP396T Imaging Technical Report

Heather Barnes

Summary

EXP396T was a transit and Tie-up. A new temperature controlled light enclosure was installed and tested on the SHIL. SHIL track IMS was updated to Version 12 to accommodate new info needed for the XSCAN and Labview was updated to 2021 on all tracks in the Core Lab. New RGB values for the 2019 Xrite color Checker standard were added to the SHIL's calibration software based on the L*ab values provided by Xrite. A new addition to the Image Correction was incorporated into the SHIL software allowing the technician to correct with more colors from the Xrite color checker. In addition a visual display of the colors using the RGB's of before and after correction has been added. The Calibration section of the SHIL User Guide was updated to reflect the new temperature controlled lights, the new RGB values of the 2019 Xrite color checker and the improved Image Correction interface.

Freight

Oncoming (received)

2 x Axio Microscopes (1 in FMBIO, 1 in FIMG)

LED for microscope (see printed note in imaging office)

T-shirt transfer paper

SEM mounts

Off-going

n/a

System Status

SHIL

Hardware

The new light enclosure developed onshore to maintain the temperature of the lights at 30°C was installed (image below). See the ETs report for in-depth description. There is a fan system to cool the lights, heaters to heat the lights and a temperature display of the lights. Repeated scanning of sections causes the temperature to increase to about 36°C. We ran multiple sections continuously to test the cooling system when scanning a section and the max temperature the lights reached was 36°C. It is important to note that when calibrating we must maintain the light's temperature close to the scanning temperature to reflect the scanning environment. We found maintaining a temperature between 30-40°C during calibration is reasonable. In addition, the new lenses help to diffuse the light from the round LED lights much better than the previous set up. This has helped the issue we were seeing with the dip in light between the round LEDS. That being said, we could not test real sections and Exp 391 will be the true test. The fwd temperature controller failed while we were off shift and the temperature of the lights reached 150°C. No damage is noted. The ET fixed the controller and it is currently working. New controllers and heaters are on order (as spares) and should arrive before EXP391.

Software

SHIL software - IMS was updated to Version 12 to include functions needed for the XSCAN. Labview was updated to 2021. In doing so several bugs were identified and fixed. Testing was completed to confirm the SHIL is in working order.

Calibration

Be sure to use the 2019 Xrite color checker mini for calibration. With the lights' new cooling system we do not have to worry about damaging the color calibration card and thus can go back tot he Xrite mini color checker (Macbeth standard) rather than the Grey QP card V101. The calibration software is set up to use the 2019 Xrite color checker. There has been a change in RGB values of the XRite color checker since 2014. Any color checker version before 2014 will not have the same RGB values that are entered into the calibration software. The new RGB values were added to the software and a link to the values is saved in the SHIL UG (under Calibration).

There are upgrades to the Image Correction interface (see image below). We now have the option to TIFF/JPG correct using extra colors on the Xrite color checker. The new feature is being discussed with the lab working group and testing needs to be completed to see if there is any benefit to using extra colors. For now continue correcting with white, the shades of grey and black. Below are some screen shots of the new user interface, please refer to the SHIL user guide Calibration section for better instructions (please update user guide as you see fit). In addition I have been investigating the illuminant of our cree lights. The current RGB values are calculated using an illuminant of D65, but this may not be the optimum correction for our lights (color temp of 4000K). The illuminant corrections that are applied when converting from L*ab vary, thus determining the illuminant of our lights may help the color corrections when using the other colors. At the time of writing this report we found that the illuminant of A is the best fit for our lights. For any further investigation, an excel spreadsheet of calculated RGB values with varying illuminants using the calculator found at http://www.brucelindbloom.com/index.html?Calc.html is saved here.

PRINTER - ECOTANK

Grey ink was added to AMS and is due to arrive in oncoming shipment. The Ecotank was used to print the Tech photo. Semigloss print setting was found to produce the best image quality.

MICROSCOPES

The new epifluorescence MBIO microscope was received and install in FMBIO. Alignment and testing needs to be completed. A second microscope and all parts are in the Imaging office.

OTHER

Floor in imaging office was sanded and painted.