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We developed an automatic method for synaptic partner identification in insect brains and use it to predict synaptic partners in a whole-brain electron microscopy dataset of the fruit fly. Those predictions can be used to infer a connectivity graph with high accuracy, thus allowing fast identification of neural pathways. To facilitate circuit reconstruction using our results, we developed CircuitMap, a user interface add-on for the circuit annotation tool Catmaid.

Brain wiring diagrams showing every individual neuron and all the synaptic connections are becoming an important resource for neuroscientists. However, only a few such high-resolution wiring diagrams have been reconstructed so far. Emerging high-throughput electron microscopy (EM) technologies have started to fill this critical gap. EM images of neural tissue with sufficiently high resolution at large scale allow the extraction of the wiring diagram. The sheer size of acquired datasets precludes manual analysis and makes the development of computer-based automatic methods necessary. In this work, we propose and test new methods to address the problem of automatic identification of microtubules and synaptic partners in large-scale EM image datasets with the ultimate goal to aid circuit reconstruction. In the first part of the thesis, we introduce a method for the automatic reconstruction of microtubules. Microtubules follow the backbone of a neuron and can be an important source of constraints for the reconstruction of neurons. We formulate an energy-based model on short candidate segments of microtubules found by a local classifier. We enumerate and score possible links between candidates, in order to find a cost-minimal subset of candidates and links by solving an integer linear program. The model provides a way to incorporate biological priors including both hard constraints (e.g. microtubules are topologically chains of links) and soft constraints (e.g. high curvature is unlikely). We test our method on a challenging EM dataset of Drosophila neural tissue and show that our model reliably tracks microtubules spanning many image sections. In the second part of the thesis, we propose a method for the prediction of synaptic partners, which is, along with the segmentation of neurons, required for circuit reconstruction. For the prediction of synaptic partners, we propose a 3D U-Net architecture to directly identify pairs of voxels that are pre- and post-synaptic to each other. To that end, we formulate the problem of synaptic partner identification as a classification problem on long-range edges between voxels to encode both the presence of a synaptic pair and its direction. This formulation allows us to directly learn from synaptic point annotations instead of the more labor-intensive voxel-based synaptic cleft or vesicle annotations. We evaluate our method on the MICCAI 2016 CREMI challenge and improve over the current state of the art, producing 3% fewer errors than the next best method. The third and last part of the thesis is also dedicated to the reconstruction of synaptic partners. Compared to the previously introduced method, we propose to directly predict post-synaptic locations and the direction to their pre-synaptic partner. We use our method to extract 244 million putative synaptic partners in the fifty-teravoxel full adult fly brain (FAFB) EM dataset and evaluated its accuracy on 146,643 synapses of 702 neurons with a total cable length of 312 mm in four different brain regions. We find that the predicted synaptic connections can be used together with a neuron segmentation to infer a connectivity graph with high accuracy. Our synaptic partner predictions for the FAFB dataset are publicly available, together with a query library allowing automatic retrieval of up- and downstream neurons. The three methods described in this work have produced state-of-the-art results on two very challenging, highly anisotropic EM datasets. The 244 million putative synaptic partners in the FAFB dataset will be a valuable resource for neuroscientists. While the fully automatic extraction of large wiring diagrams is still impeded by high accuracy requirements, this work is an important contribution for the acceleration of reconstruction efforts.

Although rectal prolapse is a rather rare disease with a low incidence, it is usually associated with a high level of suffering on the part of the affected person. Therapy is therefore of great importance. In the end, the prolapse can only be corrected adequately by surgical intervention. A variety of techniques are available for this purpose. To date, no method has been able to establish itself as the technique of choice. The decision is usually made on the basis of experience. In addition to transabdominal procedures, perineal techniques are mainly used. According to the current scientific consensus, there is no significant difference in complication and recurrence rates between the individual methods. The method evaluated in this study is Rehn-Delorme’s transanal mucosectomy and muscle tightening. In the literature, the method is associated with a low complication rate, but a relatively high recurrence rate compared to other methods. The aim of this study was to evaluate the outcome of treatment after Rehn-Delorme’s surgery by long-term evaluation. In addition to the symptoms, the course of the complaints, and surgical data, the complication and recurrence rates were of particular interest. The survey of the study group was conducted after a pretest by telephone, post and interviews. In addition, a proctological follow-up was recommended and offered. The study included a total of 54 patients who underwent rectal prolapse surgery after Rehn-Delorme between May 2011 and December 2017. The electronic medical records of all 54 patients were available for data collection. Contact was made with 48/54 patients, their relatives or their general practitioners. In the course of this, 36/48 persons were willing to participate in the survey. However, 5/48 refused to participate in the study. A further 7/48 could be recorded as deceased in the follow-up interval. Due to missing contact information 6/54 persons were not reachable and were registered as Lost to follow up. The data collected by means of questionnaires came 100 percent from female persons. The average age of the interviewees at the time of the operation was 73.9 years. The follow-up interval for the interviewed patients was 45.4 months on average. Fecal incontinence and constipation are associated with particularly high suffering. In this study, 25/36 (69.4%) of the interviewed patients suffered from preoperative stool incontinence. With regard to the course of fecal incontinence, 56.0 percent reported a lasting improvement in symptoms as a result of Rehn-Delorme’s surgery. From preoperative chronic constipation suffered 19/36 (52.8%) respondents. In summary 7/19 (36.8%) patients reported a postoperative improvement in defecation. In this study, a postoperative complication rate of 5.7 percent was recorded (n= 3 postoperative bleeding). Perioperative mortality was zero percent. The arithmetic mean of the postoperative stay was 3.5 days and that of the duration of the operation 34.0 minutes. In this study, 6/48 (12.5%) of the patients reached in the study suffered a new rectal prolapse after previous Rehn-Delorme’s surgery. Regarding the satisfaction with the surgery, 17/36 (47.2%) patients replied that they were "very satisfied" with the outcome of the surgery. A further 14/36 (38.9%) participants were "satisfied" with the operation performed. Other 3/36 (8.3%) respondents declared to be "moderately satisfied". In addition, 2/36 (5.6%) patients were "dissatisfied" with the outcome of the Rehn-Delorme procedure. The results of this study confirm the data described in the literature, whereby the recurrence rate in the present study appears to be very low. Prospective studies with a large random sample appear to make sense., Der Rektumprolaps ist zwar mit einer niedrigen Inzidenz ein eher seltenes Krankheitsbild, jedoch meist mit einem hohen Leidensdruck der betroffenen Personen assoziiert. Eine Therapie ist somit von hoher Wichtigkeit. Die Behebung des Prolapses kann letztendlich nur durch eine chirurgische Intervention adäquat erfolgen. Hierfür steht eine Vielzahl an Techniken zur Verfügung. Bis heute konnte sich keine Methode als Technik der Wahl durchsetzen. Die Entscheidung wird meist auf Grund von Erfahrung getroffen. Neben transabdominellen Verfahren kommen vor allem perineale Techniken zum Einsatz. Laut derzeitigem wissenschaftlichen Konsens besteht kein signifikanter Unterschied bezüglich Komplikations- und Rezidivrate zwischen den einzelnen Methoden. Die in dieser Studie evaluierte Methode ist die transanale Mukosektomie und Muskularisraffung nach Rehn-Delorme. In der Literatur wird das Verfahren mit einer niedrigen Komplikationsrate, jedoch im Vergleich zu anderen Verfahren mit einer relativ hohen Rezidivrate assoziiert. Ziel dieser Untersuchung war es das Behandlungsoutcome nach einer Operation nach Rehn-Delorme durch eine Langzeitevaluation zu betrachten. Neben Beschwerdebild, Verlauf der Beschwerden, operationstechnischen Daten waren vor allem die Komplikations- und Rezidivrate von hohem Interesse. Die Befragung des Studienkollektivs erfolgte nach vorangegangenen Pretest mittels Fragebogen telefonisch, per Post und in Interviews. Des Weiteren wurde eine proktologische Nachuntersuchung empfohlen und angeboten. In die Studie eingeschlossen wurden die zwischen Mai 2011 und Dezember 2017 insgesamt 54 aufgrund eines Rektumprolapses nach Rehn-Delorme operierten Patienten und Patientinnen. Die elektronischen Krankenakten aller 54 Patienten und Patientinnen konnten zur Datenerhebung eingesehen werden. Kontakt aufgenommen werden konnte mit 48/54 Patienten und Patientinnen, deren Angehörigen oder deren Hausärztinnen und Hausärzten. Im Zuge dessen waren 36/48 Personen bereit an der Befragung teilzunehmen. Es lehnten jedoch 5/48 eine Teilnahme an der Studie ab. Weitere 7/48 konnten als im Follow up Intervall verstorben verzeichnet werden. Aufgrund fehlender Kontaktinformationen waren 6/54 Personen nicht erreichbar und wurden als Lost to follow up verzeichnet. Die mittels Fragebogen erhobenen Daten stammten zu 100 Prozent von weiblichen Personen. Der Altersdurchschnitt der Befragten zum Zeitpunkt der Operation lag bei 73,9 Jahren. Das Follow-up Intervall bei den befragten Patientinnen betrug im Mittel 45,4 Monate. Mit besonders hohem Leidensdruck sind Stuhlinkontinenz und Obstipation verbunden. In dieser Studie litten 25/36 (69,4%) der befragten Patientinnen unter einer präoperativen Stuhlhalteschwäche. Bezüglich des Verlaufs der Stuhlinkontinenz berichteten 56,0 Prozent von einer dauerhaften Verbesserung der Beschwerden durch die Operation nach Rehn-Delorme. Unter einer präoperativen chronischen Obstipation litten nach eigenen Angaben zufolge 19/36 (52,8%) Befragten. Über eine postoperative Verbesserung der Stuhlentleerung konnten 7/19 (36,8%) Patientinnen berichten. In dieser Untersuchung konnte eine postoperative Komplikationsrate von 5,7 Prozent verzeichnet werden (n= 3 Nachblutungen). Die perioperative Letalität entsprach null Prozent. Das arithmetische Mittel der postoperativen Verweildauer lag bei 3,5 Tagen und das der Operationsdauer bei 34,0 Minuten. In dieser Untersuchung erlitten 6/ 48 (12,5%) der im Rahmen der Studie erreichten Patientinnen und Patienten einen erneuten Rektumprolaps nach vorangegangener Operation nach Rehn-Delorme. Bezüglich der Zufriedenheit mit der Operation, antworteten 17/36 (47,2%) Patientinnen, dass sie „sehr zufrieden“ mit dem Ergebnis des Eingriffs seien. Weitere 14/36 (38,9%) Teilnehmerinnen waren mit der durchgeführten Operation „zufrieden“. Andere 3/36 (8,3%) Befragten erklärten „mäßig zufrieden“ zu sein. Außerdem waren 2/36 (5,6%) Patientinnen „unzufrieden“ mit dem Ergebnis des Eingriffs nach Rehn-Delorme. Die Ergebnisse dieser Untersuchung bestätigen die in der Literatur beschriebenen Daten, wobei die Rezidivrate in der vorliegenden Studie sehr niedrig erscheint. Prospektive Studien mit großer Stichprobe erscheinen sinnvoll.

Trabajo presentado en la 21st International Conference Medical Image Computing and Computer Assisted Intervention, celebrada en Granada, del 16 al 20 de septiembre de 2018, High-throughput electron microscopy allows recording of large stacks of neural tissue with sufficient resolution to extract the wiring diagram of the underlying neural network. Current efforts to automate this process focus mainly on the segmentation of neurons. However, in order to recover a wiring diagram, synaptic partners need to be identified as well. This is especially challenging in insect brains like Drosophila melanogaster, where one presynaptic site is associated with multiple postsynaptic elements. Here we propose a 3D U-Net architecture to directly identify pairs of voxels that are pre- and postsynaptic to each other. To that end, we formulate the problem of synaptic partner identification as a classification problem on long-range edges between voxels to encode both the presence of a synaptic pair and its direction. This formulation allows us to directly learn from synaptic point annotations instead of more expensive voxel-based synaptic cleft or vesicle annotations. We evaluate our method on the MICCAI 2016 CREMI challenge and improve over the current state of the art, producing 3% fewer errors than the next best method (Code at: https://github.com/juliabuhmann/syntist)., This work was funded by the SNF grants P2EZP2_165241 and 205321L_160133.