[cosc-grad-students-list] iCORE Workshop: Dr. Bird - Agentic AI
Bird, Chris
chris.bird at tamucc.edu
Fri Mar 6 07:16:45 CST 2026
Hi All,
There were some questions about my log of prompting codex. I started this well after the limpetSlicer module was started and the workflow was stable. These are reverse chronological issues that I wrote out while codex cli was working on a task. When it finished, I would copy and paste in the next things to do. Some this is fixing small details. Other parts include prompts to add big features. This can be copied into a md renderer
# ADDRESSED: Documentation Issues
- Most Module UI docs don't work. On the web browser, this message comes up `Cannot find a valid ref in save_markup/LimpetAutoLandmarkEditor/Docs/LimpetAutoLandmarkEditor_UI.md` . `save_markup` is not a valid dir. if that were removed, I think the links would work. Check this for all Module UI documentation files in the Help UI.
- same thing happens for Module READMEs. `save_markup/LimpetAutoLandmarkEditor/README.md` same solution, remove `save_markup` from link path
- same thing happens for Extension READMEs. same solution as above
# ADDRESSED: Measurements Updates
when renaming below, be sure to rename all derivatives and update outputs accordingly
- rename the ApertureW line to MaxApSpanLR
- rename the ApertureL line to MaxApSpanAP
- rename the ShellH line to SpireH
- after the shell is reoriented and the lines mentioned above have been found save the following additional measurments which should be marked with a set of landmarks named Measurements which are invisible by default and the color black:
- MaxOI the maximum model value on the O axis
- MinOI the min model value on the I axis
- MinOI_A the min model value on the I axis on the anterior side of the aperture center
- MinOI_P the min model value on the I axis on the posterior side of the aperture center
- MaxOI_Aperture_L the max model value for the aperture rim on the left side of the aperture center
- MaxOI_Aperture_R the max model value for the aperture rim on the right side of the aperture center
- MaxRL the max model value on the R axis
- MinRL the min model value on the L axis
- MaxAP the max model value on the A axis
- MinAP the min model value on the P axis
- from the above measurements make the following calculations
- ShellH_AP = MaxOI - mean(MinOI_A, MinOI_P)
- ShellH_RL = MaxOI - mean(MaxOI_Aperture_R, MaxOI_Aperture_L)
- ShellL = MaxAP - MinAP
- ShellW = MaxRL - MinRL
# ADDRESSED: Issues for The ApertureL and W Lines
- I noticed a situation in eastmaui1-100N_086_2017_bench, when I rotate it -5 degrees with the model set to SpireInfrmd_RflctSymm, the widest span of the aperture from right to left is incorrect. The distance from LM 090 to 270 is obviously greater. This indicates that something is wrong with the code used to find the widest right-left span of the aperture. Consequently there must also be something wrong with code used to find the longest A-P aperture span because I believe that code is nearly identical to that for the widest span. This might be a good time to do some consolidation. I think we should just have one function to find the widest span and the arguments passed to the function should define the axis along which to find the widest or longest aperture span.
- Before we make any fixes, please update the LimpetAutoLandmarker/README.md to explicitly describe how each of the measurement lines are determined (ApertureL, ApertureW, ShellH).
- If it doesn't already, Update the AGENTS.md to note that as methods such as the determination of these lines, the center of the aperture, and the plane of symmetry, that the documentation needs to be updated to reflect the change
- while we are adjusting the lines, can we make them a different color? HOw about green
---
# ADDRESSED: LimpetAutoPseudoLMGenerator
- Let's change name of this module to LimpetBatchAutoPseudoLMGenerator. I made a mistake when I named it originally since it's only intended to be a batch processing module.
- Where are the symmetry plane options read from? Are they found based on the dir(s) in the inputs? That seems good, just making sure they aren't hardcoded
- IN the UI, move "Enforce spatial sampling rate" to PseudoLM Settings section
- When I ran this with Nested Model Dirs selected, I can't find the `pseudoLM_*tsv` and pseudoLM_manifest.json
- When I ran this with Nested Model Dirs unselected, the `pseudoLM_*tsv` and pseudoLM_manifest.json are in `*_markups` but they should be saved to `*_metadata`. I think one issue is that we don't specify the metadata output dir so all of the files are going to the only specified output dir. Let's add a Metadata output dir selector and save the metadata files there.
# ADDRESSED: LimpetAutoCreateSemiLMPatches
- As with the PseudoLMGenerator, When I ran this with Nested Model Dirs unselected, the metadata are in `*_markups` but they should be saved to `*_metadata`. I think one issue is that we don't specify the metadata output dir so all of the files are going to the only specified output dir. Let's add a Metadata output dir selector and save the metadata files there.
# ADDRESSED: LimpetBatchAutoLandmarker
- keep the present speed presets and bring back "Balanced"
---
# ADDRESSED: Issues for LimpetAutoCreateSemiLMPatches
- When nested model dirs is not checked, and the models dir is selected, if the default landmarks dir (`*_markups`) exists, it should be loaded in the landmarks dir and semilandmarks dir selectors
# ADDRESSED: Create new module: LimpetAutoPseudoLMGenerator
Let's create a new module that automates the slicermorph module PseudoLMGenerator, just like we did for CreateSemiLMPatches. The UI for inputing the models should work the same as LimpetAutoCreateSemiLMPatches. We want to provide the user with the same controls as they would have in PseudoLMGenerator:
- Spacing tolerance: slider, default = 4, min=0, max = 10
- Template Geometry: don't give an option for this, force it to be Original Geometry. Because of this, we won't need Template scale factor which are greyed out when Original Geometry is selected
- Symmetry plane: default to our Plane_000, but provide the other planes in markups as options in a drop down.
- Template scale factor: slider, default = 110, min = 75, max = 150; grey out, don't let user change when template geometry is "Original Geometry"
- Maximum projection factor: slider, default = 200, max = 200, min = 1
To run the module, let's provide the user with the ability to select the number of workers, a check box named "Enformce spatial sampling rate" that is checked by default, and if checked will trigger the slicermorph PseudoLMGenerator function Enforce spatial sampling rate. When the user clicks the "Run" button, the following slicermorph functions should be run in order:
- Get subsample number
- Generate template
- Project points to surface
- (Optional) Enforce spatial sampling rate
We want to record the settings just like we did for LimpetAutoCreateSemiLMPatches. We also want to create our own documentation for this feature, but it also makes sense to provide a link to the slicermorph documentation for PseudoLMGenerator: https://github.com/SlicerMorph/SlicerMorph/tree/master/Docs/PseudoLMGenerator<https://nam12.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2FSlicerMorph%2FSlicerMorph%2Ftree%2Fmaster%2FDocs%2FPseudoLMGenerator&data=05%7C02%7Ccosc-grad-students-list%40listserv.tamucc.edu%7C574131ba41f24afce2c408de7b829ddf%7C34cbfaf167a64781a9ca514eb2550b66%7C0%7C0%7C639083998114300847%7CUnknown%7CTWFpbGZsb3d8eyJFbXB0eU1hcGkiOnRydWUsIlYiOiIwLjAuMDAwMCIsIlAiOiJXaW4zMiIsIkFOIjoiTWFpbCIsIldUIjoyfQ%3D%3D%7C0%7C%7C%7C&sdata=YjAZ4g5duiEyi4qPDr9Ro4do29eW6g8CVd6qBOTvzoQ%3D&reserved=0>. Markups should be saved to the markups dir.
# ADDRESSED: LimpetFastBatchAutoLandmarker updates
- in the UI Settings section, add a speed preset, "Intensive" which uses the present defaults for the Advanced section fields, eg Symmetry sample N: 8000, etc...
- the default speed preset should be "Intensive"
- When user selects a different speed preset, the Advanced values should update accordingly
- the Aperture edge landmarks and Post-align Z rotation fields should be moved from Advanced to Settings.
- Remove the word "Fast" from the name of the module, code, and outputs in reference to this module. eg LimpetFastBatchAutoLandmarker should be changed to LimpetBatchAutoLandmarker.
---
# ADDRESSED: LimpetAutoLandmarkEditor
In LimpetAutoLandmarkerEditor, when "Nested Model Dirs" is not selected, the Models dir: selector
should only let the user select a dir. Presently it forces the user to choose a file. If the
default Landmark dir (*_markups), TAbles dir (*_tables), Scenes dir (*_scenes), and Metadata dir
(*_metadata) exist in the same dir as *_models, they should automatically be populated, and then the
first model should be automatically loaded. If they don't exist, then don't autoload the model. The
user will have to select each dir and then press the "Load model" button. The UI behavior when Nested
Model Dirs is check should not change.
# ADDRESSED: UI Tweaks for all modules
- Update Shell Opacity and Plane Opacity with sliders that default to 50% and range from 0 to 100%
- Update Post-align Z rotation with a slider that defaults to 0, min -180, max 180
- Update the Aperture edge landmarks to a slider with min =2, max =360, and default = 8
# ADDRESSED: Troubleshooting LimpetFastBatchAutoLandmarker
- If I don't select "Overwrite existing model output files", I get an error popup: "specimens_dir"
# ADDRESSED: Troubleshooting LimpetFastBatchAutoLandmarker
- If I don't select "Overwrite existing model output files", I get an error popup: "specimens_dir"
-
# ADDRESSED: Troubleshooting LimpetAutoLandmarker
- When I select a model it does not load automatically.
- when I select "Next model path" the next model does not load and the previous model and markups are not removed from the environment
-
## Issues for When "Nested Model Dirs" is checked in the UI
- when no data exists other than the input data, I'm getting prompted that output files already exist. I started with no output dir. LimpetAutoLandmarker makes the output dir structure (possibly on model load?) but there's no files. I think we are creating the output dir structure, then detecting it and deciding data already exists.
## Issues for When "Nested Model Dirs" is not checked in the UI
- the aggregate dir is a form of nested structure, so just put the contents of the aggregate dir in `*_metadata`
# ADDRESSED: Issues for When "Nested Model Dirs" is not checked in the UI
I have done zero troubleshooting of the modules when "Nested Model Dirs" checkbox is unchecked until now. We have to make some updates now that I'm investigating this.
## Limpet*AutoLandmarker modules
In the Output_Metadata UI, we should
- add a "Nested Output Dirs" checkbox and have it checked by default. The code here already conforms to nested output dirs, so when this is checked, the behaviors are good.
- when this is not checked, we need to add code to create a different output dir structure
- The output root does not need to change, that can serve as the root name for the output dirs
- For the modified models, the output can be in a dir named according to the output root and "_models"
- For the markups, "_markups"
- For the tables, "_tables"
- For the scenes, "_scenes"
- For the metadata and other outputs that goto the parent output dir when the box is checked, when unchecked, "_metadata"
- We should have a second checkbox "Specify output dirs". It should be unchecked by default and only visible if "Nested Output Dirs" is unchecked. when Specify output dirs is checked:
- we need fields, modeled after the "Output root" fields and button(s), that allow the user to change the output dir for models, markups, tables, scenes, and metadata. They should be autopopulated with the default dirs specified above.
- the overwrite logic needs to be updated to handle these updates and maintain original function for when the Nested Output Dirs checkbox is checked.
## LimpetAutoLandmarkEditor
When "Nested Model Dirs" is not checked in the UI, in the Inputs section we should as:
- The "Model files directory" should only allow the user to select a directory. Change label to "Models dir"
- "Landmark directory" seems good for now, but change label to "Landmark dir"
- Add a "Tables dir" selector
- Add a "Scenes dir" selector.
- Add a "Metadata dir" selector.
- Remove the "Output directory" from Inputs. If changes are made, each file type should be saved back to their input dirs. Note that these updates should go hand in hand with suggested changes for the Limpet AutoLandmarker modules
When saving data and Nested Model Dirs is unchecked, the data should be saved back to the specified input dirs. The Overwrite logic needs to be updated so that it's looking in the correct location for where data might be overwritten and maintain original function for when the Nested Model Dirs checkbox is checked.
## LimpetBatchAutoCreateSemiLMPatches
The Inputs UI works well, however, when "Nested Model Dirs" is unchecked,
- the output should not create a nested dir hierachy. Instead, the semlLMpatches and merged semiLMpatches files should be saved to the specified output dir directly.
- this also means that the "overwrite" logic should be updated to look for existing data in the specified output dir, not subdirs of the output dir
- it would be nice that if the Semilandmarks output dir is not specified that it would be autopopulated with the Landmark dir when the landmark dir is selected.
- in the UI Inputs labels, rename "directory" to "dir" and change Model to Models, Landmark to Landmarks
# ADDRESSED" Issues for LimpetAutoLandmarkEditor
When a model is loading, there is a few second delay that might prompt the user to try to click the button again. Can we let the user know that the model is loading?
# ADDRESSED: Issues for LimpetAutoCreateSemiLMPatches
- change default Max projection distanct to 25.
- in the UI change "Num workers" to "Num parallel workers"
- I dont think we are using the "Merge highlighted nodes" function to merge the semiLM patches, are we? If not, we should be doing that
- we need to record the settings used for each model when running LimpetAutoCreateSemiLMPatches, it seems like we could use semi_patch_status.tsv to record the settings
- change the output file name semi_patch_patches.tsv to semiLM_patches.tsv
- change the output file name semi_patch_status.tsv to semiLM_patches_status.tsv
# ADDRESSED: Issues for LimpetAutoCreateSemiLMPatches
- lets implement multiple workers just like we did for LimpetFastBatchAutolandmarker
# ADDRESSED: Issues for LimpetAutoCreateSemiLMPatches
- I want to expose additional slicermorph CreateSemiLMPatches UI Parameters. (1) Landmark set: so that if there are multiple landmark sets, the user can specify, but default to "Landmarks". (2) The "Max projection distance" should be controlable with a slider with a min of 0 and max of 100 and a default of 20. (3) The "Smoothing of projection vectors" should also have a slider with a min of 0 a max of 100 and a default of 0. (4) the name of the landmark to use for the second triangle lm that defines the patch, this should default to "Spire".
- it seems like we haven't saved the merged the semiLM patches. We should do that, save those to the `markups` dir in addition to the patches themselves
# ADDRESSED: Issues for LimpetBatchAutoCreateSemiLMPatches
- getting an error. models are loaded but
[Python] Batch completed with errors. See status TSV for details.
[Python] C:/Users/cbird/Downloads/limpetSlicer/data/LimpetFastBatchAutolandmarker\semi_patch_status.tsv
Could not invoke CreateSemiLMPatches with supported call signatures. Last error:
# ADDRESSED: Issues for All Modules
- the aperture length and width lines are hidden by default. I want them to be visible by default.
- the model opacity default should be 50%. Sometimes it is and sometimes it's not
# ADDRESSED: Issues for LimpetAutoLandmarkEditor
- in the UI, when I select a model dir, I'd like to also see the model files and if a model file is selected, it should just load the model dir, and regardless of whether the dir or model file is selected, it should be loaded into the environment once selected. Presently, I cannot see the model files when in the file explorer and when I select the folder, the model is not loaded. I have to select the Load Model button to load the model.
- Once the model is loaded, Anterior is towards the camera and Superior is up, but Superior should be towards the camera and Anterior should be up.
- I manually changed the env so that A was up and S was towards the camera. Then when I click "Next model directory", it does suto load the model which is desired, but it changes to Anterior down and S towards the camera. It should orient the viewer so that A is up and S is towards the camera.
- In the UI Inputs, I think we should add a Prev model directory button that behaves just like the Next model dir button, but it should go to the previous dir instead of the next dir.
- When I click next model dir or load the next model by searching the file explorer and loading the next model, the settings in the UI don't seem to update, they remain the settings from the last model. They should update to show the settings used for the model presently loaded. Make sure that the settings in the Advanced section of the UI are also those for the present model.
- IN the UI INputs section, change button labels to "Prev model" and "Next model"
- Let's keep the ShellH line hidden rather than visible by default
# ADDRESED: List of things to fix
* can you propose additional Center/Symmetry methods
For each UI that has the Advanced parameter section, add a detailed section to the readme explaining what change each setting does, how to dial them in, and what optimal parameters are.
Let's make a plan, tasks and todos to create another module called LimpetFastBatchAutolandmarker that employs your speed up ideas for the slicer gui.
Let's make a plan, tasks and todos to create another module called LimpetFastBatchAutolandmarkerCLI that employs your speed up ideas for the command line. Honestly, I'm not sure what the customary way to add cli only tools to a slicer extension, so I'm open to feedback on this one.
Let's make a plan, tasks and todos to make another module. This one is named LimpetAutoLandmarkEditor. The UI should be nearly identical to LimpetAutoLandmarker. The primary purpose of this module should be to allow a user to easily navigate the output dir structure made by LimpetAutoLandmarker and LimpetBatchAutolandmarker to allow a user to evaluate the placement of the plane of symmetry and landmarks and allow them to rerun the auto-landmarking if they want to change settings. The changes in settings and markup will need to be saved back into the dir. The inputs should be updated from LimpetAutoLandmarker in that there will only be one model in any dir, so it will have to ../NEXTDIR/nextmodel. The settings should remail the same. The Output Dir should be the same as the input dir and other than that, the output metadata section of the UI should be the same. When the model is loaded, so should all of the markup. Let me know what questions I can answer to provide any clarificaitons.
Let's make a plan, tasks and todos to make another module. This one is named LimpetBatchAutoCreateSemiLMPatches. It should use the SlicerMorph module named CreateSemiLMPatches. The slicermorph module creates triangular patches of semilandmarks given 3 landmarks. it accepts the model, the landmark set, three landmarks to define the triangle, "Select number of rows/columns in resampled grid" (default is 10), Set max projection distance, and set smoothing of projection vectors. We want to automate this module and feed in all set of three landmarks where the second landmark is the spire and the first and last landmarks are adjacent along the aperture such that the whole shell is covered by triangular patches of semilandmarks. I'm hoping that all we have to do is automate the process of running the slicermorph module. The inputs should be a dir with models and a dir with
-----Original Appointment-----
From: Khan, Ayesha <akhan4 at islander.tamucc.edu>
Sent: Tuesday, March 3, 2026 7:55 AM
To: Khan, Ayesha; Bird, Chris; Duff, Joseph; King, Scott; White, Miranda; Ciardelli, Shane
Cc: so-icore at listserv.tamucc.edu; CBI-Students; cosc-grad-students-list at listserv.tamucc.edu; csclub at listserv.tamucc.edu; cosc at listserv.tamucc.edu; Korinne Caruso; Smith, Rick; Vicens Miquel, Marina; Congo, Jose; Tissot, Philippe; Rubio Medrano, Carlos; Phadke, Abhishek; Sen, Sanjib; Habib, Ahsan; Sekharan, Chandra; Medrano, Antonio; Estrada, Beto; Heuermann, Lewis; Hadimlioglu, Alihan; bcisneros13 at webdmc.delmar.edu; Montelongo, Michaela; Lopez Morales, Efren; Demir, Kadir Alpaslan
Subject: iCORE Workshop: Dr. Bird - Agentic AI
When: Thursday, March 5, 2026 4:00 PM-5:00 PM (UTC-06:00) Central Time (US & Canada).
Where: iCORE (NRC 2100) and online
Good morning, everyone!
iCORE will be hosting a talk by Dr. Chris Bird, this Thursday (3/5) at 4:00 PM. Join us in NRC 2100 or on Teams!
Title: Agentic AI
Topic: Dr. Bird will give an overview of his experience using agentic AI with OpenCode.ai and Codex CLI: two autonomous coding agents that can be run locally from the user's terminal to read, write, and execute code. These agents function similarly to skilled contractors, allowing anyone to manage complex workflows and programming tasks. This talk will provide an insightful look into the future of research using agentic AI.
Presenter Bio: Dr. Christopher Bird is an Associate Professor of Biology at the College of Science - Department of Life Sciences. His research is focused on molecular ecology, evolution and conservation biology. He also directs the Genomics Core Laboratory, which is focused on supporting researchers in population genomics, environmental DNA, genome sequencing and assembly.
iCORE Workshops are bi-weekly starting at 4:00pm. They follow iCORE update meetings (3:30PM). All are welcome to both or either meeting.
Date
Workshop Topic
Speaker
2/19/2026
Data Compression in Social Networks
Dr. Chandra Sekharan
3/5/2026
Agentic AI
Dr Chris Bird
3/19/2026
Fog Prediction
Abdullah Bdeir
3/26/2026
Fall Detection
Leana Bouse
4/2/2026
NO meeting Leana Bouse defense at 1pm
4/16/2026
Data Visualization
Dr Scott King
4/30/2026
Data Imbalance
Dr Evan Krell
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For organizers: Meeting options<https://nam12.safelinks.protection.outlook.com/?url=https%3A%2F%2Fteams.microsoft.com%2FmeetingOptions%2F%3ForganizerId%3D4911b284-e212-43f5-ba96-e714ce86a86f%26tenantId%3D34cbfaf1-67a6-4781-a9ca-514eb2550b66%26threadId%3D19_meeting_ZTFjOWRlNzAtNGI3Ny00NGQwLWJiMTctMDcyZjM0ZmYzYTA1%40thread.v2%26messageId%3D0%26language%3Den-US&data=05%7C02%7Ccosc-grad-students-list%40listserv.tamucc.edu%7C574131ba41f24afce2c408de7b829ddf%7C34cbfaf167a64781a9ca514eb2550b66%7C0%7C0%7C639083998114426824%7CUnknown%7CTWFpbGZsb3d8eyJFbXB0eU1hcGkiOnRydWUsIlYiOiIwLjAuMDAwMCIsIlAiOiJXaW4zMiIsIkFOIjoiTWFpbCIsIldUIjoyfQ%3D%3D%7C0%7C%7C%7C&sdata=z2loQ8iAi001BEmcADfbWnuSbIM%2BKk%2FpJHb2ovij988%3D&reserved=0> | Reset dial-in PIN<https://nam12.safelinks.protection.outlook.com/?url=https%3A%2F%2Fdialin.teams.microsoft.com%2Fusp%2Fpstnconferencing&data=05%7C02%7Ccosc-grad-students-list%40listserv.tamucc.edu%7C574131ba41f24afce2c408de7b829ddf%7C34cbfaf167a64781a9ca514eb2550b66%7C0%7C0%7C639083998114447324%7CUnknown%7CTWFpbGZsb3d8eyJFbXB0eU1hcGkiOnRydWUsIlYiOiIwLjAuMDAwMCIsIlAiOiJXaW4zMiIsIkFOIjoiTWFpbCIsIldUIjoyfQ%3D%3D%7C0%7C%7C%7C&sdata=c3rO92AGBBt7eNg1fGGuTsIsmT1Ed9IFm45jhyf%2F%2BDQ%3D&reserved=0>
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