ALICE Development - Workstation/Workflow: create a working set-up for 7 Canons and Digi Cam Control

[chelseagraham]

Produce a fully working set up for all Canons that meets as many requirements as we can right now with Digi Cam Control (but is not expected to meet all, but it is still functional) by 20th September

[chelseagraham]

4 September

Source and set up 7 cameras and barcode reader in order to test if our computer is robust enough to control this number of items in the software PASS

Begin getting acquainted with digiCamControl

Begin making arrangements for trip to London to visit NHM London to discuss their current ALICE set-up and prototype for next generation ALICE set-up

[chelseagraham]

11 September

Arrange for rental of Canon R10 from Goecker for label camera to be used with one of our Canon RF 100 mm lenses

Determine logisitics of testing/camera arrangement since it is only possible to rent one R5

Test to see if possible to attribute barcode to metadata of all images taken during a session Does not seem possible

[chelseagraham]

16 September

Set up all Canons except R10 for testing Since we care most about lens cameras,

• Use 3 Canon R5 with Canon RF 100 mm lens for 3/4 label cameras (0041 with 0214; 0042 with 0059; 0215 with 0045; 0218 with 0044) Since we know we can achieve desired specimen images with Canon R5 with Canon RF 100 mm lens (our other 3 of this model body are still out for repair), but we need to challenge the program with 6 cameras,
• Use Canon 5D with Canon EF 24-70mm lens for Dorsal camera (0056 with 0058)
• Use Canon 5D with Canon EF 24 mm lens for Lateral camera (0024 with 0023)

Continue to get acquainted with digiCamControl and test for performance

[chelseagraham]

17 September

Set up Canon R10 with Canon RF 100 mm lens

Determine image settings M ISO: 100 Shutter: 0.4 Aperture: 14 White Balance: Auto Exposure Compensation: 0.0 Compression: 0 Metering Mode: Evaluative Focus: One Shot AF Drive Mode: Single-frame Shooting

Focal distance = 450-500 mm (measured from camera sensor Φ to focal plane) All label cameras raised c. 200 mm from the copy stand base to the middle of the bottom back of the camera

Begin testing file saving conventions Begin testing that we can save in the same manner as entomoloGUI (grouped in a folder for each acquisition, but by barcode instead of time)

Begin testing in digiCamControl

[chelseagraham]

18 September

Confirm file saving settings Can save all images in a folder with the barcode as a subfolder under another folder (Date>Pictures, for example) PASS

[Date yyyy-mm-dd][Barcode][Barcode]_[Camera Name] can be saved as a setting to be selected when imaging Location can also be selected Can yield, for example Pictures>digiCamContol>2024-09-19>12345678> files inside named, for example 12345678_Camera Name

So, Matilde anticipates that is will be quite easy for Digitizers to save their own presets to include their initials with the date, so no more creating new folders will be necessary.

Set up computers for capturing comparative data

entomoloGUI requires a different branch Change branch in Visual Studio Code with guidance from Lars via Slack Open Visual Studio Code > open entomoloGUI folder

• under recent files, select ~/Desktop/lworkspace/EntomoloGUI Change the branch
• click in the bottom right corner (in blue) and select canonCameraWorkspace

Discover, entomoloGUI is very specific to the exact serial number of camera, so the branch used with the all Canon test in the past is not usable for this testing

[chelseagraham]

September 19

Lars configures entomoloGUI to our array https://github.com/NHMDenmark/Pinned-Insects-workstation/issues/93#issuecomment-2360463557

01

Take Comparative Shots

where the insect remains static, but the software changes between acquisitions. Therefore, the cameras are being unplugged and replugged into the other computer between each acquisiton and the focus is being adjusted to show how results differ in achieving focus via software (digiCamControl) vs. manually via entomoloGUI

1/ Østerbolle beetle 11:27 entomoloGUI

11:32 digiCamControl (NHMD776137029)

Comparison

2/ Green Beetle 19 11:36 digiCamControl (010000386)

11:43 digiCamControl

• many issues with camera 0042 (reinitialize, turn off and on, reinitialize) back
• then issue with camera 0056 (reinitialize, turn off and on, reinitialize) back

Comparison

3/ Green Beetle 23 11:48 entomoloGUI 11:54 digiCamControl (851659047)

• program off when reconnected to PC
• Needed to turn back on, select Saving Settings and turn off and on one camera in order to get everything reconnected

4/ Side Mounted Beetle 11:58 digiCamControl (309389953) 12:02 entomoloGUI

5/ Black Beetle with Genitalia 12:06 entomoloGUI 12:10 digitCamControl (314082312)

Impressions Easier to establish focus within digiCamControl than entomoloGUI Focus appears sharper in images yielded bu digiCamControl vs. entomoloGUI Both systems perofrmed well, with minimal interruptions despite all of the unplugging The all-Canon arrays took comparable amount of time to set up vs. Pi-eyes previously had

All files at N:/SCI-SNM-DigitalCollections/DaSSCo/Development Data/Pinned Insects Working Data/ALICE/Chels_Canon_202409/2024-09-19/01_CompShots_digiCamControl and N:/SCI-SNM-DigitalCollections/DaSSCo/Development Data/Pinned Insects Working Data/ALICE/Chels_Canon_202409/2024-09-19/01_CompShots_entomoloGUI

02

Take Shots for Assessing Retention of Focus

where settings are established for the group of insects and all insects are imaged in a row, in each software

digiCamControl

Adjust focus in digiCamControl for all label cameras

• 3-5 minutes to set up

Start 12:18

Take images and note barcode in notebook for:

1/ Side Mounted Beetle (467219402) 2/ Black Beetle with Genitalia (NHMDof) 3/ Green Beetle 23 (010000344) 4/ Green Beetle 19 (220095581) 5/ Østerbolle beetle (189787139)

End 12:22

entomoloGUI

Adjust focus manually for all label cameras

• 3-5 minutes to set up

Start 12:28

1/ Side Mounted Beetle 2/ Black Beetle with Genitalia

• FAIL camera 0024 disconnected. Tried to reconnect for 10 minutes.
• Closed entomoloGUI, turned all cameras off, restarted computer

After lunch, tried trials again. First try had a fail due to Camera 0024. Reconnected and tried again.

Adjust focus manually for all label cameras

• 3-5 minutes to set up

Start 14:10

1/ Side Mounted Beetle 2/ Black Beetle with Genitalia 3/ Green Beetle 23 4/ Green Beetle 19 5/ Østerbolle beetle

End 14:13

Comparisons

Impressions Easier to establish a better focus within digiCamControl than entomoloGUI Actual acquisitions took a comprabale amount of time, but overall digiCamControl took less time due to failures with entomoloGUI

All files at N:/SCI-SNM-DigitalCollections/DaSSCo/Development Data/Pinned Insects Working Data/ALICE/Chels_Canon_202409/2024-09-19/02_RetentionFocus_digiCamControl and N:/SCI-SNM-DigitalCollections/DaSSCo/Development Data/Pinned Insects Working Data/ALICE/Chels_Canon_202409/2024-09-19/02_RetentionFocus_entomoloGUI

03

Take shots for Comparing R5 to R10

with 100 mm lens from the same angles

Camera comps

1/ Front Left R5 (0215 with 0045) R10 (Rental)

2/ Front Right R5 (0215 with 0045) R10 (Rental)

3/ Back Right R5 (0042 with 0059) R10 (Rental)

4/ Back Left R5 (0041 with 0214) R10 (Rental)

All files at N:/SCI-SNM-DigitalCollections/DaSSCo/Development Data/Pinned Insects Working Data/ALICE/Chels_Canon_202409/2024-09-19/03_R10vsR5_eachlocation