Policies & Procedures

Purdue University has made significant investment in the establishment of the Ag Alumni Seed controlled-environment phenotyping facility (AAPF) and the Indiana Corn and Soybean Innovation Center (ICSC)  in order to empower and promote research, education,  and development of products. PU faculty across the colleges and their collaborators in the public and private sectors have access to the facilities.  

Key systems in the AAPF include the hyperspectral imaging system, the RGB imaging system, and the CT-Xray root scanner system. These systems are the core sensing systems in Purdue’s broader efforts to establish high-throughput plant phenotyping platforms which provide phenotypical data across plant growth stages. These systems enable the researchers to leverage proximal plant sensing to establish measurements of intricate morphological and functional characteristics of plants.   

The Director for Digital Phenomics along with AAPF Facility Managers develop policies and procedures for the AAPF. The faculty advisory committee reviews, revises, and approves the policies and procedures. This document provides guidance to customers on the use of the facilities. The aim is to provide optimum service and to keep the communications transparent.  


  • Provide customers access to state-of-the-art facility and services to empower discoveries, education, and extension programs, and contribute to the College of Agriculture at Purdue University in its mission for global food security and sustainability in agriculture  
  • Sustain and enhance the core facility structure, operation, and service in a transparent fashion
  • Provide professional training opportunities for faculty, students, and staff
  • Strengthen public-private partnerships in research by making these facilities available and providing exceptional service to collaborators from the public and private sectors.


  • Interested user should meet with the facility manager/director digital Phenomics to provide information about the PI(s), billing information, proposed period of study, grant ID, space needed, media, chamber environment (temperature, RH, photoperiod), treatments, experimental design, species, etc. at least Three (3) months before the expected starting date. All these information will be stored in the AAPF experiment template. Once the information is gathered, the manager will find the nearest time when sufficient system space is available and environmental conditions will be compatible with the experiment’s requirements  
  • Experimental design and implementation must be discussed with the facility manager before the experiment schedule is finalized (see the attached AAPF SOP)  
  • The phenotyping space will only be assigned for the specific time period required by the project, and the assigned space cannot be reassigned to other users;  
  • When rescheduling of an experiment is needed, the facility manager must be informed 2 months before the scheduled date. If the facility manager is not informed in time, financial penalty will apply unless other projects(s) can be accommodated  
  • If/when delay in project completion is expected to occur, users should discuss with the facility manager as soon as possible  

Phenotyping equipment, and environmental controls  

  • Phenotyping equipment and the growth chambers in the AAPF are not for personal use. All the high-throughput imaging systems and the control of environmental conditions within the growth chambers (temperature, humidity, lights, ventilation, etc.) are to be operated by the staff at the AAPF only. Requirements to changes in environmental conditions should be made via emails
  • Any malfunctions in the environmental control systems or the high-throughput imaging systems occur should be immediately reported to the facility manager in person or by email  
  • Unless an emergency situation is involved, normal after hour/weekend emails will be answered within two (2) business days.   
  • Two standard pot sizes are available: 3 gallon (200 mm in height) and 6 gallon (400 mm in height). A stock of standard potting media and other common use supplies are kept on hand for AAPF projects. These supplies are available for research projects conducted at the AAPF at no extra cost. Supplies are not to be used for laboratory work, fieldwork, and/or personal use. Supplies are also dedicated to the AAPF only  
  • Project supplies and materials are prepared on a project-by-project basis. Advance notification is encouraged for special needs in pot mixes, pots, trays, etc. Nonstandard Supplies and Extras – (special media mixes, different fertilizer, etc.) can be obtained through the AAPF facility Manager and charged to the user project.   
  • Plants are imaged on Monday/Wednesday/Friday   
  • Roots are scanned on Tuesday/Thursday  
  • Plants grown out of AAPF can be imaged in AAPF too. But scheduling of these plants need to be discussed and agreed upon with the AAPF management teame  
  • When needed, if the managers are unable to get hold of the contact person or the PI of the project in a timely fashion (24 hours or less), they will have the ability to make a decision to address system failure, environmental control, pest, pathogens, etc.  
  • The automation systems may have failures beyond the staff’s control. In those cases, images are not guaranteed on scheduled days. When/if this does occur, the AAPF staff will work with the user(s) on finding solutions, which may lead to no charges being incurred, or for experiment to be repeated at no charge, but the research lab will not be reimbursed for any costs their lab incurred  
  • Pathogen and virus studies are performed on a limited basis under special conditions because of the likelihood of contamination as plants move past other experiments  
  • Plants grown in the greenhouses and imaged in the AAPF ideally should be quarantined in a dedicated GH space,  and need to be sprayed forty-eight (48) hours before they are moved into the AAPF, and be inspected by the AAPF manager twenty-four 24 hours before the scheduled imaging event.   
  • When a person visits the general greenhouses, it is highly recommended that he/she not entering AAPF within 24-hours of the visit  

AAPF Building security

  • Access to the AAPF is limited to authorized personnel only. Visitors must be properly escorted and supervised by a faculty or staff member at all times.
  • AAPF Staff members are available Monday through Friday from 8:30 am to 5:00
  • Users requiring access to the AAPF should work with to the AAPF facility Manager for authorization


  • Please provide 72-hour notice for tours led by an AAPF staff member
  • As a courtesy, please notify AAPF staff as soon as possible (e.g., 72 hours) about self-guided tours in AAPF

Phenotyping User Responsibilities  

  • Maintain open lines of communication with the AAPF Staff concerning the course or status of the project.
  • Communicate the needs of space and supply in advance, including contacting the AAPF facility manager three (3) months before the project start date.
  • Consult with the AAPF facility Manager if there is a requirement for unusual types of supplies.
  • Submit email requests for assistance, change in treatments (e.g. special watering instructions, moving plants, etc.)
  • The AAPF users are expected to maintain an active role in the progress of their projects.
  • Promptly notify the AAPF facility Manager of on observed issues or any other problems in the facility
  • Notify the AAPF facility manager promptly when a project is completed. The billing for the space will continue unless notified otherwise
  • Plant materials should be disposed or harvested within one (1) week after completion of the project. Allowing materials to become pest infested or overgrown will not be permitted in the AAPF.