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AI agent for biologists

Blot and Gel Quantification Check Agent

Consistent normalized band values in which every lane passes quality checks or is flagged with a reason.

Quality controlAnalysisScience and research
See how it worksGet access
Blot and Gel Quantification Check Agent: what goes in, what the agent does and what you get

What it does

Two people quantify the same blot and get different numbers, and a saturated band quietly ends up in a figure. This agent reads exported band intensity data and normalizes each lane to its loading control. It flags saturated bands, uneven loading, missing lanes and background that is too high. Flagged lanes go on a re-measure list with the reason. After you re-expose or rescan, it reads the new data and checks again. It then calculates the relative values by the method you set and builds a table for each blot. You approve values for the figure. Edge case: a blot where the loading control varies by more than the limit is held back until reprobed.

How it works

Follow the arrows from top to bottom. The orange dashed arrow is the loop: when a check fails, the agent goes back and tries again.

Start and resultWhat it doesA check on its own workWaits for your OKGoes back and retries
Yes, continueApprovedYes, continueApprovedNoNo 1 STARTS WHEN Intensity export loaded 2 USES A TOOL Read intensities and the lane map 3 DOES Subtract background and normalize to the loadingcontrol 4 CHECKS THE RESULT Are all lanes unsaturated with a usable loadingcontrol? If not: add flagged lanes to a re-measure list with thereason. Back to step 3. 5 YOU APPROVE Scientist approves the re-measure list 6 USES A TOOL Read new exposures or scans for the flagged lanes 7 DOES Recompute normalized values for the updated lanes 8 CHECKS THE RESULT Is loading control variation within the limit acrossthe blot? If not: hold the blot and recommend reprobing orstripping. Back to step 7. 9 DOES Build the relative value table by the chosen method 10 YOU APPROVE Scientist approves values for the figure 11 RESULT Quantification table with flags
Read the steps as a list
  1. Intensity export loaded
  2. Read intensities and the lane map
  3. Subtract background and normalize to the loading control
  4. Are all lanes unsaturated with a usable loading control?If not: add flagged lanes to a re-measure list with the reason. Back to step 3.
  5. Scientist approves the re-measure listThe agent waits here for your OK.
  6. Read new exposures or scans for the flagged lanes
  7. Recompute normalized values for the updated lanes
  8. Is loading control variation within the limit across the blot?If not: hold the blot and recommend reprobing or stripping. Back to step 7.
  9. Build the relative value table by the chosen method
  10. Scientist approves values for the figureThe agent waits here for your OK.
  11. Quantification table with flags

How it decides

A lane passes if its band is below saturation, background is acceptable and the loading control is within the allowed variation.

  • Band signal above 90 percent of the maximum: flag as saturated
  • Loading control varies by more than 20 percent across lanes: hold the blot
  • Background above half the band signal: flag as unreliable
  • Missing lane: do not average, report the lane as absent

Make it yours

Every agent is a starting point. You choose these settings for your own situation.

  • Saturation limit (default 90 percent)
  • Loading control variation limit (default 20 percent)
  • Normalization method
  • Lane map format
  • Figure table layout

What keeps you in control

It always asks you first

  • The re-measure list
  • Values used in a figure

Hard limits

  • Never drop a lane silently
  • Never change the raw image data

It stops when

  • Done: all lanes pass or are excluded with reasons
  • Stop: blot must be reprobed

Set it up

We guide you through the set-up, step by step

Members get the full set-up guide for this agent. No technical skills needed: you copy, paste and upload.

10 minto set it up in your AI
5 AIsChatGPT, Claude, Copilot, Gemini, Grok
  • One set of instructions to paste into your AI, with the clicks for ChatGPT, Claude, Microsoft 365 Copilot, Gemini and Grok
  • The agent then walks you through connecting your own data, one source at a time
  • A downloadable copy with the flow chart, the rules and the full guide
Get access to this agent

An example run

What happensA 12-lane blot showed lane 5 and lane 9 at 96 percent of maximum. The check failed. The agent listed both for a shorter exposure. New data cut lane 5 to 71 percent, but lane 9 was still over. It was excluded. The loading control varied 9 percent, so the check passed. The scientist approved values from 11 lanes for the figure with a note.

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