The Process


Below are study considerations we will help you navigate.

Sample Preparation

At TissueMetrics, we are capable of handling entire studies from animal husbandry, through tissue labeling and image analysis.


Alternatively, customers can also prepare samples on their own and send fixed tissues, wherein we will image the samples and perform any desired analyses.


Our recommended sample preparation is extremely robust, being a very simple perfusion fixation. It requires no optical clearing or special treatment of the tissue, and samples can be imaged within 24 hours of dissection. 

After fixation, the samples can be shipped at 4°C overnight in vials containing PBS and 0.1% sodium azide. Once in our facility, each sample will be examined and photographed within 3 business days to provide an initial assessment of fixation and potential disruption from tissue extraction.


It is important to note that insufficient tissue fixation can result in sub-optimal tissue sectioning and imaging. During the evaluation period we can assist in optimizing tissue fixation, if tissues are determined insufficiently fixed for serial two-photon imaging,                         


At TissueMetrics we specialize in capturing your whole tissue. Through out use of STP technology, we can provide high-resolution sampling of your data to capture the necessary details you are after. Whether you are looking to identify the distribution of a novel protein, characterize differential fluorescent signals distributions, or map processes throughout your tissue sample, we can help you identify the necessary imaging conditions that will allow you to capture your data. Two key elements that will need to be defined are your fluorophore(s) of interest and the XY and Z sampling that you will need identify their distributions throughout the tissue.

Multi-Spectral Imaging

We are capable of performing multi-spectral imaging, which allows us to simultaneously capture multiple signal profiles from your tissue sample. Whether you are interested in imaging a single target of interest, or a combination, we can help you decide the best combination of fluorophores for labeling your samples, and we will determine the best filter combination and excitation wavelength for your imaging needs. In addition to standard fluorescence imaging, we also have the capacity to capture tissue intrinsic fluorescence signals that can reveal general tissue structure (eg. autofluorescence) as well as specific tissue components such as collagen through second harmonic generation (SHG) imaging. 

XY Sampling

1.4 um/pixel
0.7 um/pixel
0.35 um/pixel


100 micron

Physical Sections

50 micron


Optical Sections


Number of Samples

Our systems are designed for high-throughput and we are capable of providing comparative imaging and analysis across multiple cohorts, easily allowing studies requiring 10's to 100's of samples.  We offer fast turn-around on sample imaging, and for longer term studies, it is possible to schedule imaging to be performed in batches as samples become available.  

The number of samples that you will need to process will be highly dependent upon whether you are looking to perform a smaller pilot study or aim to develop a complex multi-cohort multi-time series drug treatment assay. It will also be important to consider the relative variance one might expect from your tissue labeling.  During our  consultation, we can walk you through these considerations, and can help you decide the number of animals and the right imaging parameters to acquire the answers to your questions.  


Tissue Evaluation

We want to make sure you receive the high quality results you are after. To begin a new study, we will often complete an evaluation on test samples provided by the client. For the best results, all test samples should undergo similar treatment to study samples. Any alterations in sample preparation can significantly impact study results.

We will work with you and your test samples to determine optimal imaging and sectioning parameters and to assess and troubleshoot:

  • Perfusion Quality

  • Sectioning Consistency  

  • Labeling Quality

  • Signal-to-Noise

  • Wavelength and Filter Choice

The number of test samples needed and duration of evaluation period will vary depending on the complexity of the study. If you have additional questions please contact us.

Data Size

3D volumetric histology can provide an incredible amount of detail, and can also create an incredible amount of data. The final per dataset size will be highly dependent upon the image sampling parameters chosen. It is important to consider what the optimal sampling will be to resolve your targets of interest. While one may consider attempting to sample data at the highest resolution possible, this will affect the overall time and study cost, in addition to increasing the difficulty in data transfer,  visualization, computation, and storage. To give you an idea of the relative data size requirements associated with a study, please see the chart below.                        

During our consultation, and throughout the project, we will help you make determine the optimal dataset size for your sample and aims. 

Study Cost

Each of the factors discussed so far will determine the total cost of a study, some will increase the cost per sample, while others will decrease the cost. 

In particular:

  • Standard Assays - for our standard assays we can provide high confidence in the success of your given study because we have run many similar samples and have identified and removed pitfalls which can delay or result in failures. This allows for a more competitive pricing for samples processed with these assays.

  • Custom Assays - Custom assays will always have more uncertainty. However, this is the foundation of scientific discovery, and is what makes providing a successful result to a novel assay so rewarding. We know that development projects will morph and we can adapt as new information becomes available. We will work with you to set milestones, deliverables and expectations that will help us provide you with the most cost-effective project possible.

  • Data size per sample - as covered in our description of data size,  larger samples, as well as greater sampling of each tissue sample will increase the acquisition as well as storage costs per sample.

  • Labor - despite the automated nature of our techniques, labor costs are still a significant portion of our service charges. These labor costs are often front ended to each study, during the initial design and evaluation of a project. 

  • Study duration - longer duration studies and with greater numbers of samples allow us to maximize our efforts and better distribute costs, and thus provide a more competitive price per sample to our clients. 

We routinely work with groups from Academia, to Start-ups, all the way up to large Pharma, so please contact us and we’ll be happy to discuss how to best target the data you are after.

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