High-Throughput Image Analysis

The platform’s activities are supported by a professor‑researcher in biology and a PhD in physics with a Master’s degree in molecular medicine.

• Design of a comprehensive program for batch analysis of 2D–5D images from electron or optical microscopes (fluorescence and brightfield).
• 3D reconstruction of dendrites and mitochondria obtained by dual-beam electron microscopy.
• High-throughput analysis of neutrophil circulation in venous thrombosis in a murine model.
• High-throughput analysis of lung histomorphology in mice and lambs.
• High-throughput morphological characterization of microglia in the hippocampus and cortex.
• Mathematical modeling of the 3D surface of skin tumors using the Knud-Thomsen formula.
• Rigorous measurements of the susceptibility of skin cancer treated with a PARP-1 enzyme inhibitor.
• In vivo bioluminescence imaging of xenografts in an immunosuppressed murine model.
• Integration of a fleet of high-resolution microscopes and workstations into a high-speed network.
• Assembly and configuration of multi-CPU-GPU workstations.
• Repair of an in vivo small-animal imaging system and a body fat measurement device using nuclear magnetic resonance.

Equipment booking is done via the platform email address for: 

• the slide scanner (room T2-63)
• the confocal microscope (room T2-63)
• for training on equipment
• the other equipments cannot be used alone.

NOTE: the reservation of the slide scanner is managed using a queue and we notify you when the device is available. 

For your reservation, please provide the following information by email: 

• your first and last name,
• the full name of your laboratory,
• the completed form if applicable,
• your budget code (mandatory if you have one); you can request the opening of a CHUQ transit account to facilitate the payment procedure,

The platform is available to all public and private laboratories. You need to contact the platform and we will give you any useful information.

Billing is based on the time required for the instrument to acquire images from the microscopy slides. Additional unbilled time is automatically included in the time period allocated to the user to prepare for the scanning session. 

Please complete the following parameters and send the information by email. 

• Type of microscopy (fluorescence=1/brightfield=0):
• Tissue thickness* (µm):
• Slide type (single=1/double=2):
• Number(s) of slides:
• Number of planes, z =
• Channel** 1 (wavelength λ in nm or name of the fluorophore):
• Channel 2 (λ):
• Channel 3 (λ):
• Channel 4 (λ):
• Desired magnification (5,10,20 or 40):
• Average percentage of the cover slip taken by the tissue (average surface area of the ​​tissue to be imaged / entire surface area of ​​the slide × 100):
• Laboratory budget code***:

In return, you will get a time for your experience (the price is calculated based on all these parameters; it is up to the user to provide them all).

* Must be provided if the user does not carry out the experiment himself 

** Channel information only concerns fluorescence microscopy 

*** For laboratories with one 

• The standalone use of an equipment for the data acquisition from this platform requires a training which governs the rules of use.
• The resulting accreditation is individual and non-transferable.
• Equipment must be booked in advance.
• Some equipments may require an access code which will be provided. The means of access must be kept in the indicated places and not be disclosed.
• We recommend that you book the time you need as you may be charged for time you do not use (especially during periods of high demand).
• Unit reservation periods are not divisible (see the price list).
• Exceeding an established reservation period may result in an additional cost.
• Acquisition data produced by our platform or provided by you will not be stored on our servers at the end of the service. Provide a sufficient storage space before the end of the service.

In the event of a technical incident, cease operations on the instrument and immediately notify the platform manager. 

The analysis of images of all sizes generated by research laboratory instruments is our specialty. 

We invite the researcher to follow steps 1 through 8: 

1. Ask for a consultation, preferably before starting the experiment; we will be able to establish the (strongly) recommended instructions to add into your experimental protocol,
2. Acquire your images (by us or yours).
3. Prepare the images according to a precise protocol.*
4. Commission us to write/modify an algorithm specific to your image analysis needs if it is not listed in our algorithm bank.**
5. A pilot analysis will be generated from a set of your images (10 to 30).
6. Run systematic/machine learning analyses on our facilities and generate graphical visualization of statistical results.
7. Discussion on all the results and maybe repeating the analyzes can be deciced using an adjusted method or any other analysis method.
8. Obtain scientific validation of the analysis of your data.

*Analysis requires precise organization of images. Good preparation reduces errors and costs. 

**Step 4 is not required to perform routine analysis. 

The images are produced by an instrument that also records metadata: make sure this is preserved if you decide to convert the files. Their absence causes a loss of vital information for analyses. 

• The file names MUST contain all the information required by the analysis and which is not present in the metadata, i.e. experimental design information (ask us how to do or read the next answer).
• The combination of several tissues on the same slide is possible. However, the choice of tissues to put together MUST be consistent with the file name.
• Some instruments do not report, in the metadata, the coordinates of each tissue on the slide. It is recommended to produce a file for each tissue from the same slide in order to avoid significant additional analysis costs. This is particularly the case when the tissues are fragmented and difficult to individualize by a program.
• When the instrument reports tissue coordinates in each file, it is recommended to arrange the tissues on each slide in a fixed order. If possible, organize the tissues, by subject, in rows or columns along the slide.

We request the use of the rules below through an example of file name:  

2022-05-29_1234_Male!Diphtheria!DrugA(7.85mg)_H&E!DAB_BF_20X_CancerTreatmentProject.ext 

This file name is made up of 7 fields separated by “_” and ended with the file extension (czi, ndpi, tif, etc.): 

• the date in YYYY-MM-DD format,
• the identity of the sample (subject number for example),
• the value of the experiment factors separated by “!” and listed in a fixed order,
• in brightfield, the names of the markers (staining) separated by “!” » and listed in a fixed order
• the type of luminescence (“BF” or “FL”), [optional]
• magnification, [optional]
• comments. [optional]

The “_” character is not used in the field description (=prohibited). The use of spaces and commas is not recommended. 

The name structure must be constant for all files and the accuracy of the information is your responsibility. 

Contact the platform by providing the following information:

By email : analyse.images.haut.debit@crchudequebec.ulaval.ca